Starting phenix.real_space_refine on Wed Mar 4 11:22:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yov_33988/03_2026/7yov_33988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yov_33988/03_2026/7yov_33988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yov_33988/03_2026/7yov_33988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yov_33988/03_2026/7yov_33988.map" model { file = "/net/cci-nas-00/data/ceres_data/7yov_33988/03_2026/7yov_33988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yov_33988/03_2026/7yov_33988.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 8368 2.51 5 N 2307 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13232 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} bond proxies already assigned to first conformer: 570 Chain: "C" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 537 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1186 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 12, 'TRANS': 145} Chain breaks: 1 Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 516 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "A" Number of atoms: 10416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1310, 10416 Classifications: {'peptide': 1310} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1252} Chain breaks: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA D 301 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 301 " occ=0.50 Time building chain proxies: 2.85, per 1000 atoms: 0.22 Number of scatterers: 13232 At special positions: 0 Unit cell: (106.08, 159.12, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2475 8.00 N 2307 7.00 C 8368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1350 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1160 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 523.1 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 6 sheets defined 57.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 238 through 280 removed outlier: 4.277A pdb=" N ASP D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 252 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Proline residue: D 260 - end of helix removed outlier: 3.574A pdb=" N THR D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 303 Processing helix chain 'C' and resid 237 through 285 removed outlier: 3.984A pdb=" N THR C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Proline residue: C 260 - end of helix removed outlier: 4.227A pdb=" N VAL C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'E' and resid 237 through 278 removed outlier: 3.994A pdb=" N SER E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Proline residue: E 260 - end of helix removed outlier: 3.867A pdb=" N SER E 264 " --> pdb=" O PRO E 260 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET E 276 " --> pdb=" O SER E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 316 through 320 removed outlier: 3.581A pdb=" N VAL E 320 " --> pdb=" O SER E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.534A pdb=" N ASP E 340 " --> pdb=" O HIS E 337 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 341' Processing helix chain 'E' and resid 352 through 366 Processing helix chain 'E' and resid 369 through 382 removed outlier: 3.602A pdb=" N LEU E 380 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 382 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 397 removed outlier: 3.522A pdb=" N ILE E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 274 removed outlier: 3.921A pdb=" N ILE B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Proline residue: B 260 - end of helix removed outlier: 3.593A pdb=" N VAL B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.916A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.724A pdb=" N ASP A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.855A pdb=" N ARG A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.672A pdb=" N GLY A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 141 removed outlier: 4.120A pdb=" N ILE A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.531A pdb=" N CYS A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.717A pdb=" N ALA A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 254 removed outlier: 3.709A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.728A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.907A pdb=" N VAL A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 299 removed outlier: 3.518A pdb=" N PHE A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.557A pdb=" N SER A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 353 through 356 removed outlier: 3.518A pdb=" N LEU A 356 " --> pdb=" O MET A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.059A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 removed outlier: 3.619A pdb=" N GLN A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.522A pdb=" N PHE A 484 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 removed outlier: 3.581A pdb=" N LYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.704A pdb=" N PHE A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.714A pdb=" N GLU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.869A pdb=" N SER A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 removed outlier: 5.374A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.804A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.714A pdb=" N TRP A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 removed outlier: 3.832A pdb=" N HIS A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 830 removed outlier: 3.746A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.708A pdb=" N SER A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 883 removed outlier: 3.604A pdb=" N TYR A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 883 " --> pdb=" O TYR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 4.004A pdb=" N SER A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 933 through 948 removed outlier: 3.757A pdb=" N THR A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 4.096A pdb=" N MET A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 975 Processing helix chain 'A' and resid 986 through 1000 removed outlier: 3.530A pdb=" N PHE A1000 " --> pdb=" O GLN A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.763A pdb=" N GLU A1020 " --> pdb=" O ASN A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 removed outlier: 3.672A pdb=" N ALA A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1055 Processing helix chain 'A' and resid 1060 through 1070 removed outlier: 3.840A pdb=" N ILE A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1083 Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'A' and resid 1112 through 1125 removed outlier: 3.718A pdb=" N LEU A1116 " --> pdb=" O CYS A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.820A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1230 Processing helix chain 'A' and resid 1232 through 1245 removed outlier: 3.575A pdb=" N ALA A1238 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A1245 " --> pdb=" O LYS A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 4.098A pdb=" N LEU A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 4.161A pdb=" N VAL A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1328 removed outlier: 3.704A pdb=" N LEU A1318 " --> pdb=" O GLN A1314 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A1325 " --> pdb=" O LEU A1321 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A1328 " --> pdb=" O ILE A1324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310 removed outlier: 3.502A pdb=" N VAL A 384 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 382 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.648A pdb=" N GLN A 208 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 744 removed outlier: 4.367A pdb=" N ARG A 743 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 807 through 810 Processing sheet with id=AA6, first strand: chain 'A' and resid 1292 through 1294 614 hydrogen bonds defined for protein. 1765 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: 2.18 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3968 1.33 - 1.45: 2289 1.45 - 1.57: 7089 1.57 - 1.69: 0 1.69 - 1.81: 134 Bond restraints: 13480 Sorted by residual: bond pdb=" C ILE E 259 " pdb=" N PRO E 260 " ideal model delta sigma weight residual 1.336 1.394 -0.058 1.25e-02 6.40e+03 2.17e+01 bond pdb=" C ALA A 474 " pdb=" N HIS A 475 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.47e-02 4.63e+03 1.23e+01 bond pdb=" CB VAL A 748 " pdb=" CG1 VAL A 748 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.43e+00 bond pdb=" CG LEU A 647 " pdb=" CD1 LEU A 647 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.77e+00 bond pdb=" CB MET D 276 " pdb=" CG MET D 276 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.12e+00 ... (remaining 13475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 17908 3.50 - 6.99: 300 6.99 - 10.49: 35 10.49 - 13.99: 4 13.99 - 17.48: 3 Bond angle restraints: 18250 Sorted by residual: angle pdb=" CA LEU A1008 " pdb=" CB LEU A1008 " pdb=" CG LEU A1008 " ideal model delta sigma weight residual 116.30 133.78 -17.48 3.50e+00 8.16e-02 2.50e+01 angle pdb=" C GLY E 314 " pdb=" N ASP E 315 " pdb=" CA ASP E 315 " ideal model delta sigma weight residual 121.61 128.48 -6.87 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ASP A 706 " pdb=" N ASP A 707 " pdb=" CA ASP A 707 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C PHE A 580 " pdb=" N GLN A 581 " pdb=" CA GLN A 581 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" CA LEU E 286 " pdb=" CB LEU E 286 " pdb=" CG LEU E 286 " ideal model delta sigma weight residual 116.30 131.51 -15.21 3.50e+00 8.16e-02 1.89e+01 ... (remaining 18245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 7701 15.42 - 30.83: 449 30.83 - 46.24: 103 46.24 - 61.66: 13 61.66 - 77.07: 14 Dihedral angle restraints: 8280 sinusoidal: 3335 harmonic: 4945 Sorted by residual: dihedral pdb=" CB CYS A1157 " pdb=" SG CYS A1157 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual 93.00 157.59 -64.59 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA SER A1283 " pdb=" C SER A1283 " pdb=" N LEU A1284 " pdb=" CA LEU A1284 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASN A 795 " pdb=" C ASN A 795 " pdb=" N LEU A 796 " pdb=" CA LEU A 796 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 8277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1611 0.068 - 0.137: 437 0.137 - 0.205: 58 0.205 - 0.273: 10 0.273 - 0.342: 2 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE A 674 " pdb=" CA ILE A 674 " pdb=" CG1 ILE A 674 " pdb=" CG2 ILE A 674 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE D 238 " pdb=" CA ILE D 238 " pdb=" CG1 ILE D 238 " pdb=" CG2 ILE D 238 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2115 not shown) Planarity restraints: 2323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 395 " -0.024 2.00e-02 2.50e+03 2.80e-02 1.38e+01 pdb=" CG PHE A 395 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 395 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 395 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 395 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 395 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 395 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " 0.017 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A 33 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 412 " 0.019 2.00e-02 2.50e+03 1.98e-02 9.76e+00 pdb=" CG TRP A 412 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 412 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 412 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 412 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 412 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 412 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 412 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 412 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 412 " 0.001 2.00e-02 2.50e+03 ... (remaining 2320 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 240 2.66 - 3.22: 12386 3.22 - 3.78: 20834 3.78 - 4.34: 28551 4.34 - 4.90: 47088 Nonbonded interactions: 109099 Sorted by model distance: nonbonded pdb=" NE2 GLN E 255 " pdb=" OD1 ASP B 250 " model vdw 2.102 3.120 nonbonded pdb=" NH1 ARG E 263 " pdb=" OG1 THR B 261 " model vdw 2.214 3.120 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASP A 245 " model vdw 2.236 3.040 nonbonded pdb=" O GLU A 840 " pdb=" OG SER A1085 " model vdw 2.270 3.040 nonbonded pdb=" O ASP A1094 " pdb=" OG SER A1099 " model vdw 2.279 3.040 ... (remaining 109094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 236 through 300) selection = (chain 'C' and resid 236 through 300) selection = (chain 'D' and resid 236 through 300) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.011 0.103 13482 Z= 0.459 Angle : 1.167 17.484 18254 Z= 0.615 Chirality : 0.063 0.342 2118 Planarity : 0.009 0.077 2323 Dihedral : 11.203 77.075 5046 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.14 % Allowed : 3.28 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.16), residues: 1660 helix: -2.73 (0.12), residues: 884 sheet: -0.72 (0.64), residues: 71 loop : -2.53 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 562 TYR 0.038 0.004 TYR A 908 PHE 0.061 0.005 PHE A 395 TRP 0.056 0.005 TRP A 33 HIS 0.015 0.003 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.01113 (13480) covalent geometry : angle 1.16708 (18250) SS BOND : bond 0.00490 ( 2) SS BOND : angle 2.14373 ( 4) hydrogen bonds : bond 0.15613 ( 614) hydrogen bonds : angle 6.75375 ( 1765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 356 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 354 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 234 MET cc_start: 0.3778 (pmm) cc_final: 0.2844 (tpp) REVERT: B 235 MET cc_start: 0.6910 (ppp) cc_final: 0.6530 (ttm) REVERT: A 569 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 1216 LYS cc_start: 0.8173 (mttp) cc_final: 0.7717 (mtmm) outliers start: 17 outliers final: 4 residues processed: 369 average time/residue: 0.1469 time to fit residues: 72.9712 Evaluate side-chains 205 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 824 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN C 248 GLN E 279 ASN E 369 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 HIS A 222 ASN A 316 GLN A 328 GLN A 565 GLN A 575 GLN A 648 ASN A 662 ASN A 749 GLN A 775 HIS A 827 ASN A 870 ASN A 896 GLN A 906 HIS A 914 GLN A1088 HIS A1185 ASN A1375 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.170454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137365 restraints weight = 36853.150| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.96 r_work: 0.3472 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13482 Z= 0.139 Angle : 0.642 10.395 18254 Z= 0.329 Chirality : 0.043 0.228 2118 Planarity : 0.005 0.058 2323 Dihedral : 5.700 46.488 1817 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.08 % Allowed : 10.05 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1660 helix: -0.98 (0.16), residues: 879 sheet: -0.60 (0.61), residues: 71 loop : -2.03 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1220 TYR 0.021 0.002 TYR E 247 PHE 0.018 0.001 PHE A 163 TRP 0.019 0.002 TRP A 176 HIS 0.007 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00306 (13480) covalent geometry : angle 0.64090 (18250) SS BOND : bond 0.00347 ( 2) SS BOND : angle 2.11282 ( 4) hydrogen bonds : bond 0.04608 ( 614) hydrogen bonds : angle 4.70846 ( 1765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ILE cc_start: 0.4350 (mp) cc_final: 0.4114 (mt) REVERT: C 276 MET cc_start: 0.7497 (mmt) cc_final: 0.6983 (mmt) REVERT: E 354 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 234 MET cc_start: 0.3645 (pmm) cc_final: 0.2169 (tpp) REVERT: A 57 LYS cc_start: 0.8535 (tttp) cc_final: 0.8325 (tptt) REVERT: A 62 SER cc_start: 0.7610 (m) cc_final: 0.7306 (p) REVERT: A 323 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8740 (mt) REVERT: A 861 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8420 (mm) outliers start: 31 outliers final: 11 residues processed: 267 average time/residue: 0.1308 time to fit residues: 49.1052 Evaluate side-chains 203 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 38 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 652 GLN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A1315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136908 restraints weight = 32404.261| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 4.38 r_work: 0.3484 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13482 Z= 0.128 Angle : 0.592 10.559 18254 Z= 0.298 Chirality : 0.041 0.204 2118 Planarity : 0.004 0.043 2323 Dihedral : 4.990 36.315 1816 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.14 % Allowed : 11.39 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1660 helix: -0.25 (0.17), residues: 884 sheet: -0.52 (0.61), residues: 73 loop : -1.81 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 762 TYR 0.020 0.001 TYR E 247 PHE 0.018 0.001 PHE A 163 TRP 0.013 0.001 TRP A 176 HIS 0.006 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00279 (13480) covalent geometry : angle 0.59136 (18250) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.97182 ( 4) hydrogen bonds : bond 0.03949 ( 614) hydrogen bonds : angle 4.28849 ( 1765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ILE cc_start: 0.4392 (mp) cc_final: 0.4151 (mt) REVERT: D 277 GLU cc_start: 0.7821 (pt0) cc_final: 0.7592 (tm-30) REVERT: E 247 TYR cc_start: 0.5061 (t80) cc_final: 0.4515 (m-10) REVERT: B 234 MET cc_start: 0.2917 (pmm) cc_final: 0.2241 (tpp) REVERT: B 267 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6224 (tt0) REVERT: B 270 LYS cc_start: 0.8557 (tppp) cc_final: 0.8120 (tmmt) REVERT: A 35 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7615 (mp) REVERT: A 62 SER cc_start: 0.7571 (m) cc_final: 0.7259 (p) REVERT: A 101 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 111 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7650 (mmt90) REVERT: A 241 MET cc_start: 0.8861 (mmm) cc_final: 0.8536 (mmm) REVERT: A 956 MET cc_start: 0.7855 (tpt) cc_final: 0.7456 (tpt) REVERT: A 1037 VAL cc_start: 0.8421 (m) cc_final: 0.8205 (p) REVERT: A 1317 MET cc_start: 0.8107 (ttm) cc_final: 0.7698 (ttm) outliers start: 32 outliers final: 15 residues processed: 245 average time/residue: 0.1316 time to fit residues: 45.6565 Evaluate side-chains 203 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 159 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN B 267 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.165683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133053 restraints weight = 31294.754| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 4.31 r_work: 0.3448 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13482 Z= 0.161 Angle : 0.623 10.308 18254 Z= 0.311 Chirality : 0.042 0.217 2118 Planarity : 0.004 0.054 2323 Dihedral : 4.911 41.046 1814 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.48 % Allowed : 12.32 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1660 helix: 0.03 (0.17), residues: 891 sheet: -0.25 (0.64), residues: 67 loop : -1.65 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 762 TYR 0.023 0.002 TYR E 247 PHE 0.020 0.001 PHE A1360 TRP 0.012 0.001 TRP A 169 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00377 (13480) covalent geometry : angle 0.62284 (18250) SS BOND : bond 0.00281 ( 2) SS BOND : angle 1.83874 ( 4) hydrogen bonds : bond 0.03877 ( 614) hydrogen bonds : angle 4.20215 ( 1765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ILE cc_start: 0.4418 (mp) cc_final: 0.4182 (mt) REVERT: D 276 MET cc_start: 0.7620 (mtp) cc_final: 0.7228 (mtp) REVERT: E 247 TYR cc_start: 0.5088 (t80) cc_final: 0.4552 (m-10) REVERT: B 234 MET cc_start: 0.2763 (pmm) cc_final: 0.2148 (tpp) REVERT: B 267 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: B 270 LYS cc_start: 0.8566 (tppp) cc_final: 0.8097 (tmmt) REVERT: A 35 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 62 SER cc_start: 0.7705 (m) cc_final: 0.7409 (p) REVERT: A 101 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 130 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8491 (mtp180) REVERT: A 956 MET cc_start: 0.7809 (tpt) cc_final: 0.7381 (tpt) REVERT: A 1016 ASN cc_start: 0.6562 (p0) cc_final: 0.6125 (p0) outliers start: 37 outliers final: 25 residues processed: 234 average time/residue: 0.1254 time to fit residues: 41.9049 Evaluate side-chains 219 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 827 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.167348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135117 restraints weight = 25728.468| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.19 r_work: 0.3519 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13482 Z= 0.130 Angle : 0.589 10.575 18254 Z= 0.293 Chirality : 0.041 0.204 2118 Planarity : 0.004 0.045 2323 Dihedral : 4.727 41.329 1814 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.34 % Allowed : 13.13 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1660 helix: 0.29 (0.17), residues: 894 sheet: -0.21 (0.64), residues: 67 loop : -1.46 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 263 TYR 0.022 0.001 TYR E 247 PHE 0.023 0.001 PHE A 163 TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00299 (13480) covalent geometry : angle 0.58881 (18250) SS BOND : bond 0.00262 ( 2) SS BOND : angle 1.76530 ( 4) hydrogen bonds : bond 0.03691 ( 614) hydrogen bonds : angle 4.08398 ( 1765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 238 ILE cc_start: 0.4412 (mp) cc_final: 0.4191 (mt) REVERT: E 247 TYR cc_start: 0.4940 (t80) cc_final: 0.4505 (m-10) REVERT: B 234 MET cc_start: 0.2597 (pmm) cc_final: 0.2082 (tpt) REVERT: B 267 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: B 270 LYS cc_start: 0.8476 (tppp) cc_final: 0.8118 (tmmt) REVERT: A 35 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7771 (mp) REVERT: A 62 SER cc_start: 0.7503 (m) cc_final: 0.7262 (p) REVERT: A 65 ASP cc_start: 0.8263 (m-30) cc_final: 0.7917 (p0) REVERT: A 101 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 956 MET cc_start: 0.7788 (tpt) cc_final: 0.7415 (tpt) REVERT: A 1220 ARG cc_start: 0.7988 (ptm160) cc_final: 0.7519 (ptm-80) outliers start: 35 outliers final: 24 residues processed: 221 average time/residue: 0.1188 time to fit residues: 38.4160 Evaluate side-chains 210 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 143 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 ASN B 267 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134997 restraints weight = 21703.159| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.43 r_work: 0.3566 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13482 Z= 0.127 Angle : 0.578 9.760 18254 Z= 0.288 Chirality : 0.041 0.197 2118 Planarity : 0.004 0.037 2323 Dihedral : 4.628 41.687 1814 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.08 % Allowed : 12.93 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1660 helix: 0.49 (0.17), residues: 893 sheet: -0.12 (0.64), residues: 67 loop : -1.37 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.023 0.002 TYR E 247 PHE 0.027 0.001 PHE A 163 TRP 0.011 0.001 TRP A 169 HIS 0.006 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00293 (13480) covalent geometry : angle 0.57770 (18250) SS BOND : bond 0.00252 ( 2) SS BOND : angle 1.71996 ( 4) hydrogen bonds : bond 0.03592 ( 614) hydrogen bonds : angle 3.99855 ( 1765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 247 TYR cc_start: 0.5066 (t80) cc_final: 0.4476 (m-10) REVERT: B 234 MET cc_start: 0.2560 (pmm) cc_final: 0.2047 (tpt) REVERT: B 267 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6643 (tt0) REVERT: B 270 LYS cc_start: 0.8545 (tppp) cc_final: 0.8101 (tmmt) REVERT: B 298 ASP cc_start: 0.7733 (m-30) cc_final: 0.7521 (m-30) REVERT: A 35 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 62 SER cc_start: 0.7681 (m) cc_final: 0.7407 (p) REVERT: A 65 ASP cc_start: 0.8429 (m-30) cc_final: 0.7965 (p0) REVERT: A 101 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7811 (tt) REVERT: A 768 GLU cc_start: 0.7766 (tp30) cc_final: 0.7548 (tp30) REVERT: A 956 MET cc_start: 0.7816 (tpt) cc_final: 0.7405 (tpt) REVERT: A 1220 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7477 (ptm-80) outliers start: 46 outliers final: 29 residues processed: 229 average time/residue: 0.1156 time to fit residues: 39.0848 Evaluate side-chains 213 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 124 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.167846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136283 restraints weight = 32523.434| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.53 r_work: 0.3461 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13482 Z= 0.115 Angle : 0.570 10.124 18254 Z= 0.284 Chirality : 0.041 0.196 2118 Planarity : 0.004 0.042 2323 Dihedral : 4.508 41.049 1814 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.61 % Allowed : 13.73 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.21), residues: 1660 helix: 0.59 (0.17), residues: 898 sheet: -0.01 (0.65), residues: 67 loop : -1.28 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.020 0.001 TYR E 247 PHE 0.028 0.001 PHE A 163 TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00260 (13480) covalent geometry : angle 0.56986 (18250) SS BOND : bond 0.00238 ( 2) SS BOND : angle 1.68493 ( 4) hydrogen bonds : bond 0.03475 ( 614) hydrogen bonds : angle 3.97029 ( 1765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ILE cc_start: 0.4424 (mp) cc_final: 0.4171 (mt) REVERT: E 247 TYR cc_start: 0.4929 (t80) cc_final: 0.4419 (m-10) REVERT: B 234 MET cc_start: 0.2423 (pmm) cc_final: 0.2022 (tpt) REVERT: B 270 LYS cc_start: 0.8544 (tppp) cc_final: 0.8063 (tmmt) REVERT: A 35 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 62 SER cc_start: 0.7668 (m) cc_final: 0.7417 (p) REVERT: A 65 ASP cc_start: 0.8426 (m-30) cc_final: 0.7943 (p0) REVERT: A 332 ASP cc_start: 0.8074 (t0) cc_final: 0.7822 (t0) REVERT: A 749 GLN cc_start: 0.7812 (mt0) cc_final: 0.7557 (mp10) REVERT: A 956 MET cc_start: 0.7827 (tpt) cc_final: 0.7434 (tpt) REVERT: A 1017 GLU cc_start: 0.6881 (mp0) cc_final: 0.6457 (mp0) REVERT: A 1021 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8365 (mmtm) REVERT: A 1220 ARG cc_start: 0.8041 (ptm160) cc_final: 0.7415 (ptm-80) outliers start: 39 outliers final: 28 residues processed: 226 average time/residue: 0.1164 time to fit residues: 38.5984 Evaluate side-chains 213 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1034 HIS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 84 optimal weight: 0.0170 chunk 109 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 overall best weight: 0.4826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS A1235 ASN A1375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.168937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136847 restraints weight = 31319.085| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.14 r_work: 0.3488 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13482 Z= 0.107 Angle : 0.563 10.210 18254 Z= 0.280 Chirality : 0.040 0.191 2118 Planarity : 0.004 0.043 2323 Dihedral : 4.391 39.981 1814 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.21 % Allowed : 14.67 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1660 helix: 0.71 (0.17), residues: 902 sheet: 0.09 (0.65), residues: 67 loop : -1.19 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.021 0.001 TYR E 247 PHE 0.030 0.001 PHE A 163 TRP 0.010 0.001 TRP A 164 HIS 0.004 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00238 (13480) covalent geometry : angle 0.56213 (18250) SS BOND : bond 0.00230 ( 2) SS BOND : angle 1.66425 ( 4) hydrogen bonds : bond 0.03367 ( 614) hydrogen bonds : angle 3.91465 ( 1765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 247 TYR cc_start: 0.5035 (t80) cc_final: 0.4470 (m-10) REVERT: E 267 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.6287 (pt0) REVERT: B 270 LYS cc_start: 0.8515 (tppp) cc_final: 0.7973 (tmmt) REVERT: A 35 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7780 (mp) REVERT: A 62 SER cc_start: 0.7588 (m) cc_final: 0.7348 (p) REVERT: A 65 ASP cc_start: 0.8463 (m-30) cc_final: 0.7960 (p0) REVERT: A 164 TRP cc_start: 0.8913 (OUTLIER) cc_final: 0.7599 (t60) REVERT: A 241 MET cc_start: 0.8849 (mmm) cc_final: 0.8464 (mmm) REVERT: A 332 ASP cc_start: 0.8051 (t0) cc_final: 0.7801 (t0) REVERT: A 593 THR cc_start: 0.7949 (m) cc_final: 0.7680 (t) REVERT: A 956 MET cc_start: 0.7822 (tpt) cc_final: 0.7420 (tpt) REVERT: A 1220 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7347 (ptm-80) outliers start: 33 outliers final: 25 residues processed: 224 average time/residue: 0.1208 time to fit residues: 39.2064 Evaluate side-chains 213 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1034 HIS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.167640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128901 restraints weight = 34409.032| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.14 r_work: 0.3516 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13482 Z= 0.132 Angle : 0.589 10.420 18254 Z= 0.294 Chirality : 0.042 0.263 2118 Planarity : 0.004 0.037 2323 Dihedral : 4.435 41.399 1814 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.61 % Allowed : 15.14 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1660 helix: 0.72 (0.17), residues: 898 sheet: 0.13 (0.65), residues: 67 loop : -1.18 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.022 0.002 TYR E 247 PHE 0.028 0.001 PHE A 163 TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00305 (13480) covalent geometry : angle 0.58839 (18250) SS BOND : bond 0.00213 ( 2) SS BOND : angle 1.65064 ( 4) hydrogen bonds : bond 0.03513 ( 614) hydrogen bonds : angle 3.95198 ( 1765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 247 TYR cc_start: 0.4983 (t80) cc_final: 0.4433 (m-10) REVERT: E 267 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.6188 (pt0) REVERT: A 35 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 62 SER cc_start: 0.7595 (m) cc_final: 0.7359 (p) REVERT: A 65 ASP cc_start: 0.8463 (m-30) cc_final: 0.7944 (p0) REVERT: A 332 ASP cc_start: 0.7956 (t0) cc_final: 0.7740 (t0) REVERT: A 593 THR cc_start: 0.7959 (m) cc_final: 0.7702 (t) REVERT: A 871 TYR cc_start: 0.7936 (t80) cc_final: 0.7365 (t80) REVERT: A 1017 GLU cc_start: 0.6850 (mp0) cc_final: 0.6352 (mp0) REVERT: A 1021 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8332 (mmtm) REVERT: A 1087 MET cc_start: 0.8075 (mtt) cc_final: 0.7778 (mtp) REVERT: A 1220 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7298 (ptm-80) outliers start: 39 outliers final: 31 residues processed: 214 average time/residue: 0.1145 time to fit residues: 36.2040 Evaluate side-chains 213 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1034 HIS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 84 optimal weight: 0.0030 chunk 159 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 106 optimal weight: 0.0170 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.170596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138081 restraints weight = 24003.473| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.73 r_work: 0.3590 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13482 Z= 0.108 Angle : 0.569 10.265 18254 Z= 0.284 Chirality : 0.041 0.188 2118 Planarity : 0.004 0.037 2323 Dihedral : 4.271 40.614 1814 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.94 % Allowed : 16.08 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1660 helix: 0.90 (0.18), residues: 899 sheet: 0.08 (0.64), residues: 67 loop : -1.10 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.018 0.001 TYR E 247 PHE 0.028 0.001 PHE A 163 TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00239 (13480) covalent geometry : angle 0.56869 (18250) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.63158 ( 4) hydrogen bonds : bond 0.03355 ( 614) hydrogen bonds : angle 3.89428 ( 1765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 247 TYR cc_start: 0.4793 (t80) cc_final: 0.4374 (m-10) REVERT: B 283 MET cc_start: 0.8536 (tpp) cc_final: 0.7966 (tpt) REVERT: A 35 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7812 (mp) REVERT: A 62 SER cc_start: 0.7397 (m) cc_final: 0.7180 (p) REVERT: A 65 ASP cc_start: 0.8422 (m-30) cc_final: 0.7938 (p0) REVERT: A 164 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.7559 (t60) REVERT: A 241 MET cc_start: 0.8795 (mmm) cc_final: 0.8390 (mmm) REVERT: A 593 THR cc_start: 0.7823 (m) cc_final: 0.7576 (t) REVERT: A 749 GLN cc_start: 0.7686 (mt0) cc_final: 0.7464 (pm20) REVERT: A 871 TYR cc_start: 0.7877 (t80) cc_final: 0.7337 (t80) REVERT: A 1087 MET cc_start: 0.8197 (mtt) cc_final: 0.7948 (mtp) REVERT: A 1220 ARG cc_start: 0.7780 (ptm160) cc_final: 0.7211 (ptm-80) outliers start: 29 outliers final: 22 residues processed: 218 average time/residue: 0.1141 time to fit residues: 37.0038 Evaluate side-chains 204 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1034 HIS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1346 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 138 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 0.0000 chunk 27 optimal weight: 4.9990 chunk 92 optimal weight: 0.0050 chunk 121 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 HIS ** A 643 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 = 0.4193 r_free = 0.4193 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136859 restraints weight = 23872.723| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.51 r_work: 0.3587 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13482 Z= 0.112 Angle : 0.584 10.083 18254 Z= 0.294 Chirality : 0.041 0.222 2118 Planarity : 0.004 0.036 2323 Dihedral : 4.169 39.667 1812 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.81 % Allowed : 16.68 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1660 helix: 1.00 (0.18), residues: 893 sheet: 0.13 (0.65), residues: 67 loop : -1.01 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.018 0.001 TYR E 247 PHE 0.026 0.001 PHE A 163 TRP 0.010 0.001 TRP A 164 HIS 0.005 0.001 HIS A1034 Details of bonding type rmsd covalent geometry : bond 0.00248 (13480) covalent geometry : angle 0.58362 (18250) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.62327 ( 4) hydrogen bonds : bond 0.03341 ( 614) hydrogen bonds : angle 3.88134 ( 1765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.81 seconds wall clock time: 61 minutes 32.41 seconds (3692.41 seconds total)