Starting phenix.real_space_refine on Mon Mar 18 02:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eog_28375/03_2024/8eog_28375_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.80, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 7.64 Conformation dependent library (CDL) restraints added in 3.2 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... running ksdssp... Secondary structure from input PDB file: 90 helices and 14 sheets defined 47.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'D' and resid 32 through 54 Processing helix chain 'D' and resid 57 through 66 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) Processing helix chain 'D' and resid 77 through 111 Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 244 through 250 removed outlier: 4.234A pdb=" N GLY D 249 " --> pdb=" O TRP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.607A pdb=" N GLU D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 removed outlier: 3.959A pdb=" N ASN D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 Processing helix chain 'D' and resid 372 through 378 Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 418 through 426 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) removed outlier: 4.367A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 Processing helix chain 'D' and resid 434 through 443 removed outlier: 5.791A pdb=" N ASP D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.682A pdb=" N LEU D 502 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 640 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 655 through 657 No H-bonds generated for 'chain 'D' and resid 655 through 657' Processing helix chain 'D' and resid 681 through 691 Processing helix chain 'D' and resid 701 through 720 Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.931A pdb=" N GLU D 752 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 762 No H-bonds generated for 'chain 'D' and resid 760 through 762' Processing helix chain 'D' and resid 764 through 771 Processing helix chain 'D' and resid 820 through 828 Processing helix chain 'D' and resid 877 through 879 No H-bonds generated for 'chain 'D' and resid 877 through 879' Processing helix chain 'D' and resid 882 through 890 Processing helix chain 'D' and resid 1045 through 1048 No H-bonds generated for 'chain 'D' and resid 1045 through 1048' Processing helix chain 'K' and resid 113 through 120 Processing helix chain 'K' and resid 124 through 143 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 156 through 181 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 189 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 235 through 250 Proline residue: K 244 - end of helix Processing helix chain 'K' and resid 255 through 289 removed outlier: 3.579A pdb=" N VAL K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) Proline residue: K 267 - end of helix removed outlier: 5.035A pdb=" N HIS K 270 " --> pdb=" O VAL K 266 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE K 271 " --> pdb=" O PRO K 267 " (cutoff:3.500A) 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) Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 365 through 376 Processing helix chain 'K' and resid 381 through 412 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) Processing helix chain 'K' and resid 421 through 439 Processing helix chain 'K' and resid 442 through 445 No H-bonds generated for 'chain 'K' and resid 442 through 445' Processing helix chain 'K' and resid 526 through 541 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 553 through 566 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 569 through 576 Processing helix chain 'K' and resid 580 through 583 No H-bonds generated for 'chain 'K' and resid 580 through 583' Processing helix chain 'K' and resid 590 through 594 Processing helix chain 'K' and resid 596 through 608 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 613 through 632 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) removed outlier: 4.574A pdb=" N ARG K 632 " --> pdb=" O PHE K 628 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 672 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 692 through 704 Processing helix chain 'K' and resid 709 through 718 Processing helix chain 'K' and resid 728 through 762 removed outlier: 4.888A pdb=" N CYS K 739 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY K 740 " --> pdb=" O PHE K 737 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA K 759 " --> pdb=" O LEU K 756 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU K 760 " --> pdb=" O ALA K 757 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 762 " --> pdb=" O ALA K 759 " (cutoff:3.500A) Processing helix chain 'K' and resid 891 through 897 Processing helix chain 'K' and resid 901 through 916 Processing helix chain 'K' and resid 928 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 966 through 979 Processing helix chain 'K' and resid 1003 through 1010 Processing helix chain 'K' and resid 1013 through 1015 No H-bonds generated for 'chain 'K' and resid 1013 through 1015' Processing helix chain 'K' and resid 1020 through 1050 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) removed outlier: 5.849A pdb=" N ASN K1031 " --> pdb=" O ARG K1027 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE K1032 " --> pdb=" O THR K1028 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL K1033 " --> pdb=" O ILE K1029 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR K1036 " --> pdb=" O ILE K1032 " (cutoff:3.500A) Processing helix chain 'K' and resid 1066 through 1068 No H-bonds generated for 'chain 'K' and resid 1066 through 1068' Processing helix chain 'K' and resid 1105 through 1112 Processing helix chain 'K' and resid 1117 through 1125 Processing helix chain 'K' and resid 1140 through 1157 Processing helix chain 'K' and resid 1160 through 1171 Processing helix chain 'K' and resid 1184 through 1193 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 1211 through 1214 removed outlier: 3.591A pdb=" N TYR K1214 " --> pdb=" O LYS K1211 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1211 through 1214' Processing helix chain 'K' and resid 1219 through 1238 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) removed outlier: 6.021A pdb=" N ALA K1237 " --> pdb=" O THR K1233 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N MET K1238 " --> pdb=" O ILE K1234 " (cutoff:3.500A) Processing helix chain 'K' and resid 1245 through 1270 Processing helix chain 'K' and resid 1275 through 1280 removed outlier: 4.356A pdb=" N PHE K1279 " --> pdb=" O PRO K1275 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N CYS K1280 " --> pdb=" O LYS K1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1275 through 1280' Processing helix chain 'K' and resid 1282 through 1300 Processing helix chain 'K' and resid 1327 through 1341 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) removed outlier: 4.523A pdb=" N LEU K1336 " --> pdb=" O ARG K1332 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL K1337 " --> pdb=" O VAL K1333 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS K1338 " --> pdb=" O MET K1334 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU K1339 " --> pdb=" O ARG K1335 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU K1340 " --> pdb=" O LEU K1336 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER K1341 " --> pdb=" O VAL K1337 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1327 through 1341' Processing helix chain 'K' and resid 1345 through 1355 Processing helix chain 'K' and resid 1358 through 1381 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 1402 through 1414 Processing helix chain 'K' and resid 1418 through 1424 Processing helix chain 'K' and resid 1450 through 1482 removed outlier: 3.858A pdb=" N VAL K1453 " --> pdb=" O SER K1450 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER K1458 " --> pdb=" O TYR K1455 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP K1480 " --> pdb=" O ASP K1477 " (cutoff:3.500A) Processing helix chain 'K' and resid 1491 through 1503 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 1514 through 1521 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 1558 through 1569 Processing helix chain 'K' and resid 1578 through 1584 removed outlier: 4.803A pdb=" N GLU K1583 " --> pdb=" O GLU K1579 " (cutoff:3.500A) Processing helix chain 'K' and resid 1586 through 1588 No H-bonds generated for 'chain 'K' and resid 1586 through 1588' Processing helix chain 'K' and resid 1599 through 1602 Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 246 through 262 Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.928A pdb=" N SER C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 315 through 327 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 342 through 360 removed outlier: 3.773A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 70 through 74 Processing sheet with id= B, first strand: chain 'D' and resid 167 through 169 removed outlier: 7.132A pdb=" N VAL D 468 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL D 489 " --> pdb=" O LEU D 466 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU D 466 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 411 through 415 removed outlier: 3.685A pdb=" N TYR D 411 " --> pdb=" O VAL D 386 " (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: 6.589A pdb=" N ASN D 292 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL D 260 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D 294 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 461 through 463 Processing sheet with id= E, first strand: chain 'D' and resid 513 through 518 removed outlier: 3.593A pdb=" N PHE D 515 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 586 through 595 Processing sheet with id= G, first strand: chain 'D' and resid 743 through 745 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: 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= H, first strand: chain 'D' and resid 1018 through 1021 removed outlier: 3.716A pdb=" N MET D 863 " --> pdb=" O ILE D 854 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 894 through 901 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) Processing sheet with id= J, first strand: chain 'D' and resid 904 through 906 removed outlier: 3.944A pdb=" N SER D 904 " --> pdb=" O CYS D 976 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'K' and resid 1072 through 1075 Processing sheet with id= M, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.670A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 213 through 216 778 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 8.26 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=" 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=" O26 WO9 K1705 " pdb=" P25 WO9 K1705 " ideal model delta sigma weight residual 1.510 1.460 0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" O27 WO9 K1705 " pdb=" P25 WO9 K1705 " ideal model delta sigma weight residual 1.510 1.460 0.050 2.00e-02 2.50e+03 6.24e+00 bond pdb=" O21 WNZ K1704 " pdb=" P19 WNZ K1704 " ideal model delta sigma weight residual 1.510 1.460 0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" O20 WNZ K1704 " pdb=" P19 WNZ K1704 " ideal model delta sigma weight residual 1.510 1.460 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 20154 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.86: 325 104.86 - 112.17: 10063 112.17 - 119.49: 6766 119.49 - 126.80: 9939 126.80 - 134.12: 240 Bond angle restraints: 27333 Sorted by residual: 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 angle pdb=" C LYS K1077 " pdb=" CA LYS K1077 " pdb=" CB LYS K1077 " ideal model delta sigma weight residual 116.54 112.27 4.27 1.15e+00 7.56e-01 1.38e+01 angle pdb=" C GLU K1080 " pdb=" N VAL K1081 " pdb=" CA VAL K1081 " ideal model delta sigma weight residual 121.97 127.95 -5.98 1.80e+00 3.09e-01 1.10e+01 ... (remaining 27328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.28: 11609 30.28 - 60.57: 712 60.57 - 90.85: 38 90.85 - 121.13: 4 121.13 - 151.41: 3 Dihedral angle restraints: 12366 sinusoidal: 5282 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 12363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2879 0.080 - 0.159: 241 0.159 - 0.239: 5 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: 1412 2.73 - 3.28: 20936 3.28 - 3.82: 32118 3.82 - 4.36: 37346 4.36 - 4.90: 62131 Nonbonded interactions: 153943 Sorted by model distance: nonbonded pdb=" O ILE K 600 " pdb=" OG1 THR K 603 " model vdw 2.193 2.440 nonbonded pdb=" OH TYR D 452 " pdb=" OG1 THR D 463 " model vdw 2.210 2.440 nonbonded pdb=" O SER K1094 " pdb=" OG SER K1094 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR D 513 " pdb=" OE2 GLU D 567 " model vdw 2.241 2.440 nonbonded pdb=" O SER D 892 " pdb=" OG SER D 892 " model vdw 2.251 2.440 ... (remaining 153938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 6.730 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: 18.260 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 54.190 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.070 ------------------------------------------------------------------------------- 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 0.065 20159 Z= 0.209 Angle : 0.592 9.820 27333 Z= 0.300 Chirality : 0.043 0.398 3126 Planarity : 0.004 0.060 3428 Dihedral : 17.719 151.414 7752 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 2.334 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: 0.3291 time to fit residues: 71.4332 Evaluate side-chains 119 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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: 0.2980 chunk 182 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20159 Z= 0.322 Angle : 0.619 9.334 27333 Z= 0.319 Chirality : 0.044 0.268 3126 Planarity : 0.005 0.056 3428 Dihedral : 8.942 138.845 3130 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.06 % Favored : 91.81 % Rotamer: Outliers : 3.83 % Allowed : 27.59 % Favored : 68.58 % 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: -1.00 (0.17), residues: 2394 helix: 0.53 (0.16), residues: 1124 sheet: -0.41 (0.37), residues: 219 loop : -2.09 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 195 HIS 0.005 0.001 HIS D1006 PHE 0.017 0.002 PHE K 628 TYR 0.017 0.002 TYR K 938 ARG 0.009 0.000 ARG D 691 *********************** 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 197 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 115 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: D 311 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: D 508 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8008 (mt) REVERT: D 1012 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8840 (t0) REVERT: K 290 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7217 (p90) REVERT: K 629 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8631 (mmmt) REVERT: K 952 MET cc_start: 0.6419 (ppp) cc_final: 0.6145 (mmm) REVERT: K 1080 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7661 (pp20) REVERT: K 1353 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8445 (t80) REVERT: K 1400 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: K 1426 MET cc_start: 0.8280 (mmt) cc_final: 0.8043 (mmt) REVERT: K 1546 MET cc_start: 0.2987 (tpp) cc_final: 0.2726 (tpp) REVERT: C 320 MET cc_start: 0.7451 (ppp) cc_final: 0.7208 (tpp) outliers start: 82 outliers final: 50 residues processed: 192 average time/residue: 0.2948 time to fit residues: 90.5260 Evaluate side-chains 168 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 110 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 492 VAL 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 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 150 ASP Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 248 VAL Chi-restraints excluded: chain K residue 251 VAL 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 347 ASP 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 619 LEU Chi-restraints excluded: chain K residue 629 LYS Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 643 SER Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 1002 VAL 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 1353 PHE Chi-restraints excluded: chain K residue 1396 ASN 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 D residue 1108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 182 optimal weight: 9.9990 chunk 149 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 924 GLN ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1580 GLN C 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20159 Z= 0.146 Angle : 0.551 10.722 27333 Z= 0.279 Chirality : 0.041 0.315 3126 Planarity : 0.004 0.057 3428 Dihedral : 8.004 129.999 3130 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.81 % Favored : 93.07 % Rotamer: Outliers : 3.64 % Allowed : 28.43 % Favored : 67.93 % 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: -0.79 (0.18), residues: 2394 helix: 0.69 (0.16), residues: 1130 sheet: -0.24 (0.37), residues: 217 loop : -1.99 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 195 HIS 0.002 0.001 HIS D1006 PHE 0.021 0.001 PHE K 395 TYR 0.013 0.001 TYR K1278 ARG 0.006 0.000 ARG K 418 *********************** 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 195 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 117 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 PHE cc_start: 0.6101 (t80) cc_final: 0.5871 (t80) REVERT: D 311 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: D 650 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8750 (mm) REVERT: K 290 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7308 (p90) REVERT: K 629 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8582 (tppt) REVERT: K 952 MET cc_start: 0.6635 (ppp) cc_final: 0.6378 (mmm) REVERT: K 1223 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7689 (t80) REVERT: K 1399 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6458 (t80) REVERT: K 1400 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: K 1546 MET cc_start: 0.3089 (OUTLIER) cc_final: 0.2775 (tpp) REVERT: C 302 ARG cc_start: 0.7083 (tpm170) cc_final: 0.6870 (tpt170) outliers start: 78 outliers final: 35 residues processed: 185 average time/residue: 0.2894 time to fit residues: 85.5782 Evaluate side-chains 150 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 107 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain K residue 290 PHE 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 629 LYS 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 992 ASN Chi-restraints excluded: chain K residue 1106 MET Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1396 ASN 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 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 216 optimal weight: 0.0270 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 316 ASN D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 924 GLN ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20159 Z= 0.150 Angle : 0.547 9.379 27333 Z= 0.275 Chirality : 0.041 0.225 3126 Planarity : 0.004 0.056 3428 Dihedral : 7.586 124.402 3130 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.81 % Favored : 93.07 % Rotamer: Outliers : 4.01 % Allowed : 28.43 % Favored : 67.55 % 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: -0.71 (0.18), residues: 2394 helix: 0.79 (0.16), residues: 1129 sheet: -0.16 (0.37), residues: 217 loop : -1.99 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 195 HIS 0.003 0.001 HIS K1493 PHE 0.026 0.001 PHE K1161 TYR 0.020 0.001 TYR K 938 ARG 0.005 0.000 ARG K 418 *********************** 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 201 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 115 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: D 650 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8731 (mm) REVERT: K 290 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7337 (p90) REVERT: K 952 MET cc_start: 0.6661 (ppp) cc_final: 0.6305 (mmm) REVERT: K 1223 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7616 (t80) REVERT: K 1399 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6422 (t80) REVERT: K 1400 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: K 1546 MET cc_start: 0.3086 (OUTLIER) cc_final: 0.2797 (tpp) REVERT: C 196 MET cc_start: 0.7788 (mmt) cc_final: 0.7353 (mmt) REVERT: C 238 ILE cc_start: 0.1131 (OUTLIER) cc_final: 0.0757 (mt) outliers start: 86 outliers final: 53 residues processed: 192 average time/residue: 0.3066 time to fit residues: 94.1314 Evaluate side-chains 167 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 106 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 124 VAL 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 313 ASN Chi-restraints excluded: chain D residue 381 ASP 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 581 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN 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 894 TYR Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 251 VAL 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 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 543 SER 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 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 1002 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 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 1396 ASN 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 1472 VAL Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1546 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 161 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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 ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20159 Z= 0.215 Angle : 0.568 12.462 27333 Z= 0.287 Chirality : 0.042 0.222 3126 Planarity : 0.004 0.054 3428 Dihedral : 7.440 121.936 3126 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.69 % Favored : 92.19 % Rotamer: Outliers : 4.58 % Allowed : 27.82 % Favored : 67.60 % 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: -0.77 (0.18), residues: 2394 helix: 0.77 (0.16), residues: 1127 sheet: -0.22 (0.38), residues: 205 loop : -2.03 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 195 HIS 0.003 0.001 HIS D1006 PHE 0.018 0.001 PHE K 628 TYR 0.014 0.001 TYR D 514 ARG 0.006 0.000 ARG K 418 *********************** 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 209 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 111 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: D 650 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 1012 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8823 (t0) REVERT: K 199 ASP cc_start: 0.8050 (m-30) cc_final: 0.7563 (m-30) REVERT: K 200 PHE cc_start: 0.7856 (t80) cc_final: 0.7317 (t80) REVERT: K 290 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7320 (p90) REVERT: K 632 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6804 (ttm170) REVERT: K 952 MET cc_start: 0.6810 (ppp) cc_final: 0.6387 (mmm) REVERT: K 1223 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7749 (t80) REVERT: K 1278 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6611 (t80) REVERT: K 1399 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6573 (t80) REVERT: K 1400 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: K 1546 MET cc_start: 0.3077 (tpp) cc_final: 0.2800 (tpp) REVERT: C 196 MET cc_start: 0.7820 (mmt) cc_final: 0.7387 (mmt) REVERT: C 238 ILE cc_start: 0.1132 (OUTLIER) cc_final: 0.0762 (mt) outliers start: 98 outliers final: 66 residues processed: 201 average time/residue: 0.2961 time to fit residues: 95.3902 Evaluate side-chains 184 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 108 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN 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 851 ASP Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1012 ASN Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 251 VAL 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 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 543 SER Chi-restraints excluded: chain K residue 545 HIS Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 632 ARG Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 643 SER 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 1002 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 1129 THR 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 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1301 THR Chi-restraints excluded: chain K residue 1346 ILE Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1396 ASN 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 1472 VAL Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 233 optimal weight: 40.0000 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20159 Z= 0.153 Angle : 0.554 10.420 27333 Z= 0.279 Chirality : 0.041 0.230 3126 Planarity : 0.004 0.055 3428 Dihedral : 7.252 117.645 3126 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.81 % Favored : 93.07 % Rotamer: Outliers : 4.48 % Allowed : 28.01 % Favored : 67.51 % 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: -0.74 (0.18), residues: 2394 helix: 0.77 (0.16), residues: 1132 sheet: -0.16 (0.39), residues: 205 loop : -2.01 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 195 HIS 0.002 0.001 HIS D1006 PHE 0.029 0.001 PHE K 628 TYR 0.022 0.001 TYR K 938 ARG 0.006 0.000 ARG K 418 *********************** 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 206 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 110 time to evaluate : 2.336 Fit side-chains revert: symmetry clash REVERT: D 311 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: D 650 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8739 (mm) REVERT: K 200 PHE cc_start: 0.7896 (t80) cc_final: 0.7414 (t80) REVERT: K 290 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7378 (p90) REVERT: K 682 MET cc_start: 0.7084 (tpp) cc_final: 0.6858 (tpt) REVERT: K 952 MET cc_start: 0.6572 (ppp) cc_final: 0.6202 (mmm) REVERT: K 1223 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7703 (t80) REVERT: K 1278 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6617 (t80) REVERT: K 1399 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6475 (t80) REVERT: K 1400 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: K 1546 MET cc_start: 0.3143 (OUTLIER) cc_final: 0.2842 (tpp) REVERT: C 196 MET cc_start: 0.7844 (mmt) cc_final: 0.7433 (mmt) REVERT: C 238 ILE cc_start: 0.1200 (OUTLIER) cc_final: 0.0826 (mt) outliers start: 96 outliers final: 59 residues processed: 196 average time/residue: 0.3088 time to fit residues: 98.4784 Evaluate side-chains 172 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 104 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 248 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 381 ASP 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 581 ILE Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN 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 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 251 VAL 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 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 543 SER Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 643 SER 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 1002 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 1129 THR 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 1233 THR Chi-restraints excluded: chain K residue 1234 ILE Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1301 THR Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1396 ASN 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 1472 VAL Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1546 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 316 THR 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 224 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 232 optimal weight: 30.0000 chunk 145 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20159 Z= 0.292 Angle : 0.603 9.516 27333 Z= 0.309 Chirality : 0.044 0.417 3126 Planarity : 0.004 0.054 3428 Dihedral : 7.474 127.789 3126 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.06 % Favored : 91.81 % Rotamer: Outliers : 4.25 % Allowed : 27.59 % Favored : 68.16 % 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: -0.88 (0.17), residues: 2394 helix: 0.68 (0.16), residues: 1135 sheet: -0.27 (0.38), residues: 205 loop : -2.13 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 187 HIS 0.005 0.001 HIS D1006 PHE 0.029 0.002 PHE K 628 TYR 0.017 0.001 TYR D 219 ARG 0.006 0.000 ARG K 418 *********************** 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 203 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 112 time to evaluate : 2.228 Fit side-chains revert: symmetry clash REVERT: D 650 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8815 (mm) REVERT: D 1012 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8830 (t0) REVERT: K 200 PHE cc_start: 0.7890 (t80) cc_final: 0.7495 (t80) REVERT: K 632 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6841 (ttm170) REVERT: K 952 MET cc_start: 0.6739 (ppp) cc_final: 0.6282 (mmm) REVERT: K 1223 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7721 (t80) REVERT: K 1278 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6654 (t80) REVERT: K 1399 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6824 (t80) REVERT: K 1400 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: K 1546 MET cc_start: 0.3178 (OUTLIER) cc_final: 0.2905 (tpp) outliers start: 91 outliers final: 70 residues processed: 196 average time/residue: 0.2996 time to fit residues: 95.2359 Evaluate side-chains 184 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 106 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 381 ASP 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 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 679 THR 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 851 ASP Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1001 CYS 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 150 ASP Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 256 VAL 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 543 SER Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 632 ARG Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 643 SER 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 1002 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1129 THR 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 1233 THR 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 1396 ASN 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 1472 VAL 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 D residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.0170 chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1040 GLN ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20159 Z= 0.146 Angle : 0.567 9.539 27333 Z= 0.286 Chirality : 0.041 0.379 3126 Planarity : 0.004 0.055 3428 Dihedral : 7.150 118.954 3126 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 3.73 % Allowed : 28.48 % Favored : 67.79 % 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: -0.69 (0.18), residues: 2394 helix: 0.80 (0.16), residues: 1127 sheet: -0.11 (0.37), residues: 217 loop : -2.00 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP K 440 HIS 0.004 0.001 HIS K 545 PHE 0.031 0.001 PHE K1497 TYR 0.024 0.001 TYR K 938 ARG 0.008 0.000 ARG C 302 *********************** 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 191 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 111 time to evaluate : 2.362 Fit side-chains revert: symmetry clash REVERT: D 311 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: D 650 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8749 (mm) REVERT: K 200 PHE cc_start: 0.7894 (t80) cc_final: 0.7616 (t80) REVERT: K 443 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.5544 (tp-100) REVERT: K 632 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6780 (ttm170) REVERT: K 952 MET cc_start: 0.6699 (ppp) cc_final: 0.6268 (mmm) REVERT: K 1223 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7638 (t80) REVERT: K 1278 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6594 (t80) REVERT: K 1399 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6560 (t80) REVERT: K 1400 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: K 1546 MET cc_start: 0.3149 (OUTLIER) cc_final: 0.2846 (tpp) REVERT: C 238 ILE cc_start: 0.1240 (OUTLIER) cc_final: 0.0863 (mt) outliers start: 80 outliers final: 54 residues processed: 184 average time/residue: 0.2934 time to fit residues: 86.7922 Evaluate side-chains 170 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 106 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 381 ASP 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 581 ILE Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 251 VAL 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 400 VAL Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 443 GLN Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 543 SER Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 632 ARG 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 1040 GLN Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1129 THR 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 1233 THR 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 1396 ASN 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 1472 VAL Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1546 MET Chi-restraints excluded: chain C residue 238 ILE 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 222 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20159 Z= 0.380 Angle : 0.642 9.541 27333 Z= 0.329 Chirality : 0.045 0.360 3126 Planarity : 0.005 0.053 3428 Dihedral : 7.500 127.766 3126 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.52 % Favored : 91.35 % Rotamer: Outliers : 3.97 % Allowed : 28.15 % Favored : 67.88 % 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: -0.96 (0.17), residues: 2394 helix: 0.63 (0.16), residues: 1133 sheet: -0.46 (0.37), residues: 209 loop : -2.16 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 440 HIS 0.005 0.001 HIS D1006 PHE 0.034 0.002 PHE K1497 TYR 0.019 0.002 TYR D 219 ARG 0.007 0.000 ARG K 418 *********************** 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 193 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 108 time to evaluate : 2.428 Fit side-chains revert: symmetry clash REVERT: D 650 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8825 (mm) REVERT: K 200 PHE cc_start: 0.7935 (t80) cc_final: 0.7691 (t80) REVERT: K 545 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8155 (m170) REVERT: K 632 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6852 (ttm170) REVERT: K 952 MET cc_start: 0.6765 (ppp) cc_final: 0.6268 (mmm) REVERT: K 1042 MET cc_start: 0.8244 (ttm) cc_final: 0.8004 (ttm) REVERT: K 1223 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7616 (t80) REVERT: K 1278 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6581 (t80) REVERT: K 1399 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6829 (t80) REVERT: K 1400 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: K 1546 MET cc_start: 0.3218 (tpp) cc_final: 0.2928 (tpp) REVERT: C 196 MET cc_start: 0.8052 (mmt) cc_final: 0.7679 (mmt) REVERT: C 238 ILE cc_start: 0.1207 (OUTLIER) cc_final: 0.0853 (mt) outliers start: 85 outliers final: 65 residues processed: 184 average time/residue: 0.2848 time to fit residues: 85.7076 Evaluate side-chains 179 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 106 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 381 ASP 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 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 ASN 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 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 251 VAL 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 543 SER Chi-restraints excluded: chain K residue 545 HIS Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 632 ARG Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 643 SER 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 992 ASN Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1086 ILE 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 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1233 THR 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 1396 ASN 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 1426 MET Chi-restraints excluded: chain K residue 1472 VAL Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 108 optimal weight: 0.2980 chunk 159 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20159 Z= 0.147 Angle : 0.589 11.093 27333 Z= 0.294 Chirality : 0.042 0.360 3126 Planarity : 0.004 0.057 3428 Dihedral : 7.059 116.624 3126 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 2.94 % Allowed : 29.23 % Favored : 67.83 % 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: -0.69 (0.18), residues: 2394 helix: 0.82 (0.16), residues: 1123 sheet: -0.13 (0.37), residues: 217 loop : -2.01 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 187 HIS 0.005 0.001 HIS K 545 PHE 0.031 0.001 PHE K 628 TYR 0.025 0.001 TYR K 938 ARG 0.012 0.000 ARG C 302 ********************** 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 170 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 107 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: D 650 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8735 (mm) REVERT: D 885 MET cc_start: 0.8754 (tpt) cc_final: 0.8141 (tpt) REVERT: K 200 PHE cc_start: 0.7914 (t80) cc_final: 0.7690 (t80) REVERT: K 290 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7318 (p90) REVERT: K 625 LEU cc_start: 0.9181 (mt) cc_final: 0.8641 (tt) REVERT: K 632 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6838 (ttm170) REVERT: K 952 MET cc_start: 0.6769 (ppp) cc_final: 0.6242 (mmm) REVERT: K 1042 MET cc_start: 0.8148 (ttm) cc_final: 0.7931 (ttm) REVERT: K 1278 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6506 (t80) REVERT: K 1399 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6667 (t80) REVERT: K 1400 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: K 1546 MET cc_start: 0.3180 (tpp) cc_final: 0.2887 (tpp) REVERT: C 196 MET cc_start: 0.7980 (mmt) cc_final: 0.7679 (mmt) REVERT: C 238 ILE cc_start: 0.1220 (OUTLIER) cc_final: 0.0856 (mt) outliers start: 63 outliers final: 52 residues processed: 165 average time/residue: 0.3027 time to fit residues: 80.0890 Evaluate side-chains 163 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 104 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 381 ASP 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 581 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 650 LEU 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 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 251 VAL 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 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 543 SER Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 632 ARG 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 992 ASN Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1129 THR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1233 THR 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 1396 ASN 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 1472 VAL Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 196 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1040 GLN ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 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 = 0.4081 r_free = 0.4081 target = 0.110638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073808 restraints weight = 57854.534| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.02 r_work: 0.3005 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20159 Z= 0.141 Angle : 0.564 10.793 27333 Z= 0.281 Chirality : 0.041 0.351 3126 Planarity : 0.004 0.068 3428 Dihedral : 6.729 107.497 3126 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 3.03 % Allowed : 29.18 % Favored : 67.79 % 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: -0.68 (0.18), residues: 2394 helix: 0.85 (0.16), residues: 1128 sheet: -0.05 (0.37), residues: 211 loop : -2.04 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 187 HIS 0.005 0.001 HIS K 545 PHE 0.031 0.001 PHE K1497 TYR 0.011 0.001 TYR K1278 ARG 0.007 0.000 ARG K 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.06 seconds wall clock time: 79 minutes 6.70 seconds (4746.70 seconds total)