Starting phenix.real_space_refine on Wed Jan 14 22:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ae6_15381/01_2026/8ae6_15381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ae6_15381/01_2026/8ae6_15381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ae6_15381/01_2026/8ae6_15381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ae6_15381/01_2026/8ae6_15381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ae6_15381/01_2026/8ae6_15381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ae6_15381/01_2026/8ae6_15381.map" } resolution = 2.7 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= 0.014 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 98 5.16 5 C 12763 2.51 5 N 3296 2.21 5 O 3631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19788 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4641 Classifications: {'peptide': 563} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 535} Chain breaks: 6 Chain: "Q" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4073 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 471} Chain breaks: 4 Chain: "W" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7786 Classifications: {'peptide': 941} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 901} Chain breaks: 11 Chain: "S" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3288 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain breaks: 3 Time building chain proxies: 4.08, per 1000 atoms: 0.21 Number of scatterers: 19788 At special positions: 0 Unit cell: (130.68, 122.694, 159.72, 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 98 16.00 O 3631 8.00 N 3296 7.00 C 12763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.42 Conformation dependent library (CDL) restraints added in 614.0 milliseconds 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 31 sheets defined 34.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'U' and resid 33 through 39 Processing helix chain 'U' and resid 365 through 376 Processing helix chain 'U' and resid 382 through 387 removed outlier: 3.645A pdb=" N GLU U 387 " --> pdb=" O ILE U 384 " (cutoff:3.500A) Processing helix chain 'U' and resid 401 through 409 Processing helix chain 'U' and resid 526 through 530 Processing helix chain 'U' and resid 545 through 557 Processing helix chain 'U' and resid 557 through 573 Processing helix chain 'U' and resid 573 through 591 removed outlier: 3.801A pdb=" N SER U 577 " --> pdb=" O SER U 573 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 598 removed outlier: 3.981A pdb=" N GLN U 597 " --> pdb=" O SER U 593 " (cutoff:3.500A) Processing helix chain 'U' and resid 601 through 617 Processing helix chain 'U' and resid 618 through 632 Processing helix chain 'U' and resid 678 through 683 Processing helix chain 'U' and resid 743 through 747 removed outlier: 3.626A pdb=" N ASN U 746 " --> pdb=" O ASP U 743 " (cutoff:3.500A) Processing helix chain 'U' and resid 754 through 763 Processing helix chain 'U' and resid 764 through 766 No H-bonds generated for 'chain 'U' and resid 764 through 766' Processing helix chain 'U' and resid 770 through 782 Processing helix chain 'U' and resid 788 through 792 Processing helix chain 'U' and resid 793 through 798 removed outlier: 3.594A pdb=" N ASP U 798 " --> pdb=" O TYR U 794 " (cutoff:3.500A) Processing helix chain 'U' and resid 815 through 831 Processing helix chain 'U' and resid 889 through 902 Processing helix chain 'U' and resid 907 through 915 Processing helix chain 'U' and resid 922 through 926 Processing helix chain 'U' and resid 932 through 946 Processing helix chain 'U' and resid 961 through 975 removed outlier: 3.505A pdb=" N LYS U 965 " --> pdb=" O ASP U 961 " (cutoff:3.500A) Processing helix chain 'U' and resid 1080 through 1091 removed outlier: 3.753A pdb=" N ILE U1091 " --> pdb=" O LEU U1087 " (cutoff:3.500A) Processing helix chain 'U' and resid 1095 through 1105 Processing helix chain 'U' and resid 1114 through 1123 Processing helix chain 'U' and resid 1125 through 1136 Processing helix chain 'Q' and resid 267 through 271 removed outlier: 3.551A pdb=" N ALA Q 271 " --> pdb=" O GLY Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 348 Processing helix chain 'Q' and resid 401 through 407 Processing helix chain 'Q' and resid 429 through 441 Processing helix chain 'Q' and resid 503 through 523 Processing helix chain 'Q' and resid 529 through 537 Processing helix chain 'W' and resid 160 through 167 Processing helix chain 'W' and resid 177 through 184 Processing helix chain 'W' and resid 199 through 203 removed outlier: 3.663A pdb=" N GLN W 203 " --> pdb=" O PHE W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 217 through 228 Processing helix chain 'W' and resid 286 through 290 removed outlier: 3.542A pdb=" N MET W 289 " --> pdb=" O THR W 286 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP W 290 " --> pdb=" O ASP W 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 286 through 290' Processing helix chain 'W' and resid 298 through 306 Processing helix chain 'W' and resid 307 through 319 Processing helix chain 'W' and resid 338 through 342 Processing helix chain 'W' and resid 366 through 386 removed outlier: 4.661A pdb=" N ARG W 382 " --> pdb=" O PHE W 378 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS W 383 " --> pdb=" O MET W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 408 through 418 Processing helix chain 'W' and resid 419 through 421 No H-bonds generated for 'chain 'W' and resid 419 through 421' Processing helix chain 'W' and resid 449 through 461 Processing helix chain 'W' and resid 522 through 527 Processing helix chain 'W' and resid 552 through 563 Processing helix chain 'W' and resid 859 through 866 Processing helix chain 'W' and resid 887 through 891 Processing helix chain 'W' and resid 904 through 909 Processing helix chain 'W' and resid 931 through 947 removed outlier: 3.797A pdb=" N LEU W 935 " --> pdb=" O THR W 931 " (cutoff:3.500A) Processing helix chain 'W' and resid 954 through 961 Processing helix chain 'W' and resid 1053 through 1063 Processing helix chain 'W' and resid 1090 through 1094 Processing helix chain 'W' and resid 1104 through 1122 Processing helix chain 'W' and resid 1151 through 1159 removed outlier: 3.619A pdb=" N PHE W1155 " --> pdb=" O PRO W1151 " (cutoff:3.500A) Processing helix chain 'W' and resid 1387 through 1405 removed outlier: 3.630A pdb=" N TYR W1405 " --> pdb=" O LEU W1401 " (cutoff:3.500A) Processing helix chain 'W' and resid 1416 through 1423 Proline residue: W1421 - end of helix Processing helix chain 'W' and resid 1446 through 1453 Processing helix chain 'W' and resid 1455 through 1465 Processing helix chain 'W' and resid 1551 through 1560 Processing helix chain 'W' and resid 1561 through 1578 Processing helix chain 'S' and resid 34 through 39 Processing helix chain 'S' and resid 46 through 51 Processing helix chain 'S' and resid 82 through 84 No H-bonds generated for 'chain 'S' and resid 82 through 84' Processing helix chain 'S' and resid 104 through 123 Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 196 through 211 Processing helix chain 'S' and resid 260 through 267 Processing helix chain 'S' and resid 268 through 270 No H-bonds generated for 'chain 'S' and resid 268 through 270' Processing helix chain 'S' and resid 275 through 283 Processing helix chain 'S' and resid 286 through 300 Processing helix chain 'S' and resid 320 through 325 Processing helix chain 'S' and resid 329 through 339 removed outlier: 3.523A pdb=" N ASP S 333 " --> pdb=" O LEU S 329 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR S 339 " --> pdb=" O GLN S 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 345 through 349 Processing helix chain 'S' and resid 434 through 444 Processing helix chain 'S' and resid 450 through 458 Processing helix chain 'S' and resid 459 through 465 Processing helix chain 'S' and resid 468 through 479 Processing helix chain 'S' and resid 569 through 582 Processing helix chain 'S' and resid 585 through 594 Processing helix chain 'S' and resid 596 through 608 Processing sheet with id=AA1, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.673A pdb=" N VAL U 538 " --> pdb=" O LEU U 11 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR S 62 " --> pdb=" O THR U 423 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR S 73 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE S 91 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER S 88 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE S 14 " --> pdb=" O GLU S 30 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU S 30 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR S 16 " --> pdb=" O LYS S 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 23 through 25 removed outlier: 3.763A pdb=" N MET U 532 " --> pdb=" O SER U 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 636 through 640 Processing sheet with id=AA4, first strand: chain 'U' and resid 655 through 656 Processing sheet with id=AA5, first strand: chain 'U' and resid 748 through 751 Processing sheet with id=AA6, first strand: chain 'U' and resid 846 through 848 Processing sheet with id=AA7, first strand: chain 'U' and resid 1071 through 1073 removed outlier: 4.364A pdb=" N ILE U 958 " --> pdb=" O ILE U1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 304 through 312 removed outlier: 4.159A pdb=" N ASP Q 334 " --> pdb=" O SER Q 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 29 through 32 removed outlier: 3.585A pdb=" N ALA Q 29 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 73 through 75 removed outlier: 3.693A pdb=" N PHE Q 108 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASN Q 97 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE Q 106 " --> pdb=" O ASN Q 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 117 through 122 removed outlier: 3.526A pdb=" N TYR Q 152 " --> pdb=" O ALA Q 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 161 through 166 removed outlier: 6.746A pdb=" N SER Q 177 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL Q 164 " --> pdb=" O ALA Q 175 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA Q 175 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TRP Q 166 " --> pdb=" O VAL Q 173 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL Q 173 " --> pdb=" O TRP Q 166 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE Q 182 " --> pdb=" O SER Q 196 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 196 " --> pdb=" O ILE Q 182 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL Q 184 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 204 through 209 removed outlier: 4.504A pdb=" N THR Q 225 " --> pdb=" O SER Q 221 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR Q 241 " --> pdb=" O THR Q 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 248 through 253 removed outlier: 4.007A pdb=" N ARG Q 250 " --> pdb=" O MET Q 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL Q 272 " --> pdb=" O PHE Q 297 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 445 through 450 removed outlier: 6.530A pdb=" N CYS Q 457 " --> pdb=" O GLU Q 447 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE Q 449 " --> pdb=" O GLU Q 455 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU Q 455 " --> pdb=" O ILE Q 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 102 through 104 Processing sheet with id=AB8, first strand: chain 'W' and resid 107 through 109 removed outlier: 6.425A pdb=" N GLY W 107 " --> pdb=" O ILE W 174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 257 through 258 removed outlier: 6.161A pdb=" N VAL W 207 " --> pdb=" O ILE W 271 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ARG W 273 " --> pdb=" O VAL W 207 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE W 209 " --> pdb=" O ARG W 273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 231 through 234 removed outlier: 3.587A pdb=" N THR W 231 " --> pdb=" O ILE W 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 238 through 239 removed outlier: 3.622A pdb=" N GLY W 247 " --> pdb=" O LEU W 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'W' and resid 400 through 401 removed outlier: 3.757A pdb=" N ARG W 400 " --> pdb=" O ASP W 333 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER W 331 " --> pdb=" O ILE W 285 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG W 278 " --> pdb=" O HIS W 435 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N MET W 437 " --> pdb=" O ARG W 278 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE W 280 " --> pdb=" O MET W 437 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE W 439 " --> pdb=" O ILE W 280 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU W 282 " --> pdb=" O ILE W 439 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASP W 468 " --> pdb=" O THR W 434 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL W 436 " --> pdb=" O ASP W 468 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE W 470 " --> pdb=" O VAL W 436 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE W 438 " --> pdb=" O ILE W 470 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 400 through 401 removed outlier: 3.757A pdb=" N ARG W 400 " --> pdb=" O ASP W 333 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE W 324 " --> pdb=" O ASP W 360 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP W 360 " --> pdb=" O ILE W 324 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE W 326 " --> pdb=" O VAL W 358 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N LEU W1028 " --> pdb=" O SER W 351 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP W 353 " --> pdb=" O LEU W1028 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS W1030 " --> pdb=" O ASP W 353 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE W 355 " --> pdb=" O LYS W1030 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG W1038 " --> pdb=" O VAL W1029 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 387 through 389 Processing sheet with id=AC6, first strand: chain 'W' and resid 445 through 447 removed outlier: 6.492A pdb=" N PHE W 446 " --> pdb=" O ARG W 484 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ARG W 486 " --> pdb=" O PHE W 446 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS W 494 " --> pdb=" O ILE W 851 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 898 through 899 removed outlier: 3.578A pdb=" N ILE W 899 " --> pdb=" O ILE W 950 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR W 987 " --> pdb=" O CYS W 951 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL W1007 " --> pdb=" O HIS W 917 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 1344 through 1350 removed outlier: 3.909A pdb=" N TYR W1367 " --> pdb=" O ASN W1345 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS W1378 " --> pdb=" O ASP W1368 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE W1377 " --> pdb=" O VAL W1082 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS W1079 " --> pdb=" O ILE W1412 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 1340 through 1342 removed outlier: 5.636A pdb=" N LEU W1341 " --> pdb=" O MET W1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'W' and resid 1430 through 1432 removed outlier: 3.824A pdb=" N LEU W1519 " --> pdb=" O VAL W1430 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR W1507 " --> pdb=" O HIS W1502 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 213 through 217 Processing sheet with id=AD3, first strand: chain 'S' and resid 244 through 247 Processing sheet with id=AD4, first strand: chain 'S' and resid 314 through 317 removed outlier: 4.392A pdb=" N ILE S 314 " --> pdb=" O CYS S 485 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6014 1.34 - 1.45: 3330 1.45 - 1.57: 10775 1.57 - 1.69: 0 1.69 - 1.81: 151 Bond restraints: 20270 Sorted by residual: bond pdb=" N TYR U1070 " pdb=" CA TYR U1070 " ideal model delta sigma weight residual 1.452 1.477 -0.024 1.25e-02 6.40e+03 3.81e+00 bond pdb=" C VAL S 267 " pdb=" N PRO S 268 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.01e+00 bond pdb=" CA VAL S 267 " pdb=" C VAL S 267 " ideal model delta sigma weight residual 1.523 1.536 -0.013 9.20e-03 1.18e+04 1.93e+00 bond pdb=" C PHE W 308 " pdb=" N PRO W 309 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.88e+00 bond pdb=" CB ARG S 443 " pdb=" CG ARG S 443 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 ... (remaining 20265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 26965 2.06 - 4.11: 411 4.11 - 6.17: 38 6.17 - 8.23: 19 8.23 - 10.29: 6 Bond angle restraints: 27439 Sorted by residual: angle pdb=" C VAL W1022 " pdb=" CA VAL W1022 " pdb=" CB VAL W1022 " ideal model delta sigma weight residual 110.13 113.69 -3.56 9.70e-01 1.06e+00 1.34e+01 angle pdb=" C SER Q 156 " pdb=" N TRP Q 157 " pdb=" CA TRP Q 157 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C LEU W 242 " pdb=" N ASP W 243 " pdb=" CA ASP W 243 " ideal model delta sigma weight residual 122.61 127.83 -5.22 1.56e+00 4.11e-01 1.12e+01 angle pdb=" CA ILE W1420 " pdb=" C ILE W1420 " pdb=" N PRO W1421 " ideal model delta sigma weight residual 118.88 123.98 -5.10 1.54e+00 4.22e-01 1.10e+01 angle pdb=" N ILE W1420 " pdb=" CA ILE W1420 " pdb=" C ILE W1420 " ideal model delta sigma weight residual 108.88 115.49 -6.61 2.16e+00 2.14e-01 9.37e+00 ... (remaining 27434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 10925 17.65 - 35.30: 1093 35.30 - 52.95: 167 52.95 - 70.60: 17 70.60 - 88.25: 11 Dihedral angle restraints: 12213 sinusoidal: 5084 harmonic: 7129 Sorted by residual: dihedral pdb=" CA VAL U 837 " pdb=" C VAL U 837 " pdb=" N ILE U 838 " pdb=" CA ILE U 838 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA HIS W 322 " pdb=" C HIS W 322 " pdb=" N THR W 323 " pdb=" CA THR W 323 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLU W1483 " pdb=" C GLU W1483 " pdb=" N PHE W1484 " pdb=" CA PHE W1484 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 12210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2483 0.064 - 0.127: 483 0.127 - 0.191: 48 0.191 - 0.254: 5 0.254 - 0.318: 2 Chirality restraints: 3021 Sorted by residual: chirality pdb=" CG LEU W 412 " pdb=" CB LEU W 412 " pdb=" CD1 LEU W 412 " pdb=" CD2 LEU W 412 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB THR W 138 " pdb=" CA THR W 138 " pdb=" OG1 THR W 138 " pdb=" CG2 THR W 138 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE W1552 " pdb=" CA ILE W1552 " pdb=" CG1 ILE W1552 " pdb=" CG2 ILE W1552 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3018 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 75 " 0.027 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP Q 75 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 75 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 75 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 75 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 75 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 75 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 75 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 75 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 75 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS U1068 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C HIS U1068 " -0.056 2.00e-02 2.50e+03 pdb=" O HIS U1068 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP U1069 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE W1412 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO W1413 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO W1413 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO W1413 " 0.040 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3510 2.77 - 3.30: 17130 3.30 - 3.84: 33524 3.84 - 4.37: 39440 4.37 - 4.90: 68404 Nonbonded interactions: 162008 Sorted by model distance: nonbonded pdb=" OG SER Q 134 " pdb=" OD1 ASP Q 136 " model vdw 2.239 3.040 nonbonded pdb=" OG SER Q 162 " pdb=" OG SER Q 177 " model vdw 2.291 3.040 nonbonded pdb=" O VAL U 667 " pdb=" OH TYR U 862 " model vdw 2.305 3.040 nonbonded pdb=" O PHE W 415 " pdb=" OG1 THR W 418 " model vdw 2.307 3.040 nonbonded pdb=" O HIS U 28 " pdb=" OH TYR U 610 " model vdw 2.314 3.040 ... (remaining 162003 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 26.330 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: 0.420 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 17.920 Find NCS groups from input model: 0.070 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:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.004 0.046 20270 Z= 0.167 Angle : 0.635 10.286 27439 Z= 0.331 Chirality : 0.050 0.318 3021 Planarity : 0.005 0.073 3474 Dihedral : 13.855 88.252 7573 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.38 (0.16), residues: 2353 helix: -0.89 (0.16), residues: 774 sheet: -0.24 (0.23), residues: 526 loop : -1.18 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 471 TYR 0.023 0.001 TYR S 337 PHE 0.029 0.002 PHE U 408 TRP 0.067 0.002 TRP Q 75 HIS 0.005 0.001 HIS W 431 Details of bonding type rmsd covalent geometry : bond 0.00372 (20270) covalent geometry : angle 0.63469 (27439) hydrogen bonds : bond 0.19455 ( 792) hydrogen bonds : angle 7.53839 ( 2196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 0.750 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: U 376 ASP cc_start: 0.6382 (t0) cc_final: 0.6059 (t0) REVERT: U 415 MET cc_start: 0.8264 (mtp) cc_final: 0.8049 (mtm) REVERT: U 584 LYS cc_start: 0.7435 (tmmt) cc_final: 0.6802 (tmmt) REVERT: U 588 ARG cc_start: 0.6962 (ttt-90) cc_final: 0.6497 (mtt-85) REVERT: U 616 LYS cc_start: 0.7506 (mmmt) cc_final: 0.7282 (tppp) REVERT: U 754 GLU cc_start: 0.7010 (mp0) cc_final: 0.6727 (mp0) REVERT: U 787 ILE cc_start: 0.8341 (tt) cc_final: 0.8096 (pt) REVERT: U 927 ILE cc_start: 0.8637 (mt) cc_final: 0.8433 (mt) REVERT: U 931 GLU cc_start: 0.6963 (mp0) cc_final: 0.6548 (mp0) REVERT: U 1083 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7845 (mt-10) REVERT: U 1084 LYS cc_start: 0.8081 (mttp) cc_final: 0.7719 (pttp) REVERT: U 1091 ILE cc_start: 0.7716 (mm) cc_final: 0.7393 (pp) REVERT: U 1116 GLU cc_start: 0.7973 (mp0) cc_final: 0.7637 (mp0) REVERT: U 1129 LEU cc_start: 0.8292 (tp) cc_final: 0.8034 (tt) REVERT: Q 22 LYS cc_start: 0.8251 (tptt) cc_final: 0.7623 (tppp) REVERT: Q 24 ASP cc_start: 0.7572 (m-30) cc_final: 0.7303 (m-30) REVERT: Q 119 ASP cc_start: 0.7660 (t70) cc_final: 0.7357 (t0) REVERT: Q 202 SER cc_start: 0.7960 (t) cc_final: 0.7527 (p) REVERT: Q 238 SER cc_start: 0.8431 (m) cc_final: 0.8202 (t) REVERT: Q 240 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6758 (mtt180) REVERT: Q 359 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7792 (mmtp) REVERT: Q 363 TYR cc_start: 0.8206 (m-80) cc_final: 0.7949 (m-80) REVERT: Q 478 SER cc_start: 0.7751 (m) cc_final: 0.7539 (t) REVERT: Q 480 ASN cc_start: 0.7344 (t0) cc_final: 0.7091 (m-40) REVERT: Q 509 GLU cc_start: 0.7088 (tt0) cc_final: 0.6819 (tt0) REVERT: Q 530 GLU cc_start: 0.7082 (tp30) cc_final: 0.6850 (tp30) REVERT: W 195 LEU cc_start: 0.6768 (tp) cc_final: 0.6049 (mp) REVERT: W 269 ARG cc_start: 0.6874 (mtm180) cc_final: 0.6607 (mtm-85) REVERT: W 287 ASP cc_start: 0.6994 (t70) cc_final: 0.6661 (t0) REVERT: W 292 PHE cc_start: 0.8085 (m-80) cc_final: 0.7804 (m-80) REVERT: W 384 ASP cc_start: 0.7413 (m-30) cc_final: 0.7178 (m-30) REVERT: W 389 GLN cc_start: 0.7940 (tp40) cc_final: 0.7618 (tp40) REVERT: W 489 GLU cc_start: 0.7241 (mp0) cc_final: 0.6865 (mp0) REVERT: W 551 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7632 (mmtt) REVERT: W 555 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7217 (mm-30) REVERT: W 562 LYS cc_start: 0.7999 (tttp) cc_final: 0.7797 (ttmm) REVERT: W 901 ASP cc_start: 0.6523 (m-30) cc_final: 0.6141 (m-30) REVERT: W 993 GLU cc_start: 0.8253 (pt0) cc_final: 0.8047 (pt0) REVERT: W 1459 VAL cc_start: 0.8116 (t) cc_final: 0.7793 (p) REVERT: W 1487 MET cc_start: 0.4194 (mtp) cc_final: 0.3370 (mtp) REVERT: W 1575 MET cc_start: 0.5630 (mtp) cc_final: 0.5247 (mtp) REVERT: S 29 TYR cc_start: 0.6793 (m-80) cc_final: 0.6588 (m-80) REVERT: S 65 TYR cc_start: 0.8598 (t80) cc_final: 0.8217 (t80) REVERT: S 85 ASN cc_start: 0.7352 (t0) cc_final: 0.7026 (t0) REVERT: S 86 PHE cc_start: 0.8027 (p90) cc_final: 0.7806 (p90) REVERT: S 220 GLU cc_start: 0.7709 (mp0) cc_final: 0.7499 (mp0) REVERT: S 271 ASP cc_start: 0.7959 (p0) cc_final: 0.7725 (p0) REVERT: S 322 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.8265 (ttt-90) REVERT: S 440 ASP cc_start: 0.7784 (m-30) cc_final: 0.7553 (m-30) REVERT: S 571 GLU cc_start: 0.7249 (mp0) cc_final: 0.6813 (mp0) REVERT: S 572 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6221 (tm-30) REVERT: S 601 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7657 (mt-10) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.6010 time to fit residues: 418.2120 Evaluate side-chains 503 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN U 547 ASN U 921 GLN U 938 ASN U1094 GLN Q 163 GLN Q 429 ASN Q 525 ASN W 116 ASN W 255 ASN W 398 ASN W 547 ASN W 558 ASN W1059 GLN W1154 ASN W1345 ASN W1471 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.150846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133511 restraints weight = 28860.371| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.86 r_work: 0.3694 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20270 Z= 0.270 Angle : 0.610 7.955 27439 Z= 0.321 Chirality : 0.049 0.178 3021 Planarity : 0.005 0.055 3474 Dihedral : 4.729 38.644 2610 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.22 % Allowed : 12.37 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.70 (0.17), residues: 2353 helix: 0.12 (0.18), residues: 796 sheet: -0.26 (0.23), residues: 537 loop : -0.94 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W1077 TYR 0.021 0.002 TYR W 485 PHE 0.029 0.002 PHE U 408 TRP 0.032 0.002 TRP Q 75 HIS 0.007 0.001 HIS W1427 Details of bonding type rmsd covalent geometry : bond 0.00636 (20270) covalent geometry : angle 0.61024 (27439) hydrogen bonds : bond 0.04589 ( 792) hydrogen bonds : angle 5.51335 ( 2196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 536 time to evaluate : 0.721 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: U 376 ASP cc_start: 0.6613 (t0) cc_final: 0.6292 (t0) REVERT: U 584 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7175 (tmmt) REVERT: U 588 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7191 (mtt-85) REVERT: U 754 GLU cc_start: 0.7253 (mp0) cc_final: 0.7009 (mp0) REVERT: U 774 ILE cc_start: 0.8029 (mm) cc_final: 0.7746 (pt) REVERT: U 793 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7486 (mtp180) REVERT: U 897 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8008 (mp) REVERT: U 1091 ILE cc_start: 0.7826 (mm) cc_final: 0.7424 (pp) REVERT: Q 119 ASP cc_start: 0.7890 (t70) cc_final: 0.7652 (t0) REVERT: Q 202 SER cc_start: 0.8203 (t) cc_final: 0.7985 (p) REVERT: Q 240 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7159 (mtt180) REVERT: Q 287 LYS cc_start: 0.7242 (tptt) cc_final: 0.7007 (tptt) REVERT: Q 359 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7892 (mmtp) REVERT: Q 363 TYR cc_start: 0.8343 (m-80) cc_final: 0.8085 (m-80) REVERT: Q 478 SER cc_start: 0.8026 (m) cc_final: 0.7518 (p) REVERT: Q 509 GLU cc_start: 0.7300 (tt0) cc_final: 0.7076 (tt0) REVERT: W 195 LEU cc_start: 0.6857 (tp) cc_final: 0.6115 (mp) REVERT: W 235 MET cc_start: 0.7177 (tpp) cc_final: 0.6942 (tpp) REVERT: W 269 ARG cc_start: 0.7383 (mtm180) cc_final: 0.7147 (mtm-85) REVERT: W 287 ASP cc_start: 0.7144 (t70) cc_final: 0.6786 (t0) REVERT: W 302 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7835 (mtpt) REVERT: W 389 GLN cc_start: 0.7959 (tp40) cc_final: 0.7680 (tp40) REVERT: W 489 GLU cc_start: 0.7618 (mp0) cc_final: 0.7312 (mp0) REVERT: W 517 THR cc_start: 0.7869 (p) cc_final: 0.7584 (t) REVERT: W 549 LYS cc_start: 0.7934 (tmmm) cc_final: 0.7684 (tmmm) REVERT: W 551 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7759 (mmtt) REVERT: W 901 ASP cc_start: 0.6887 (m-30) cc_final: 0.6560 (m-30) REVERT: W 905 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7412 (tmtt) REVERT: W 1367 TYR cc_start: 0.7466 (p90) cc_final: 0.7186 (p90) REVERT: W 1575 MET cc_start: 0.5980 (mtp) cc_final: 0.5621 (mtp) REVERT: S 65 TYR cc_start: 0.8648 (t80) cc_final: 0.8239 (t80) REVERT: S 85 ASN cc_start: 0.7485 (t0) cc_final: 0.7231 (t0) REVERT: S 119 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8023 (mm-30) REVERT: S 124 LEU cc_start: 0.8513 (tt) cc_final: 0.8250 (tp) REVERT: S 126 SER cc_start: 0.8101 (p) cc_final: 0.7767 (m) REVERT: S 301 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8100 (mmmm) REVERT: S 345 LYS cc_start: 0.8204 (mptt) cc_final: 0.8003 (mptt) REVERT: S 440 ASP cc_start: 0.7665 (m-30) cc_final: 0.7465 (m-30) REVERT: S 571 GLU cc_start: 0.7449 (mp0) cc_final: 0.7026 (mp0) REVERT: S 572 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6444 (tm-30) outliers start: 50 outliers final: 21 residues processed: 553 average time/residue: 0.6098 time to fit residues: 381.4538 Evaluate side-chains 536 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 514 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 653 GLN Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 945 GLN Chi-restraints excluded: chain U residue 966 MET Chi-restraints excluded: chain Q residue 134 SER Chi-restraints excluded: chain Q residue 343 SER Chi-restraints excluded: chain Q residue 412 MET Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1011 LEU Chi-restraints excluded: chain W residue 1348 VAL Chi-restraints excluded: chain W residue 1471 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 457 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 212 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 218 optimal weight: 0.0050 chunk 162 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 121 optimal weight: 0.0980 chunk 216 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 921 GLN U1094 GLN Q 163 GLN Q 172 ASN Q 180 ASN ** W 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 267 GLN W 350 ASN W 916 ASN W 981 ASN W1056 GLN W1059 GLN W1154 ASN W1471 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.153973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135809 restraints weight = 28924.322| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.98 r_work: 0.3721 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20270 Z= 0.122 Angle : 0.521 7.389 27439 Z= 0.270 Chirality : 0.044 0.165 3021 Planarity : 0.004 0.052 3474 Dihedral : 4.411 36.195 2610 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.40 % Allowed : 15.52 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.34 (0.17), residues: 2353 helix: 0.58 (0.19), residues: 790 sheet: -0.17 (0.23), residues: 531 loop : -0.80 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W1012 TYR 0.014 0.001 TYR S 299 PHE 0.022 0.001 PHE U 408 TRP 0.020 0.001 TRP Q 229 HIS 0.003 0.001 HIS Q 300 Details of bonding type rmsd covalent geometry : bond 0.00282 (20270) covalent geometry : angle 0.52060 (27439) hydrogen bonds : bond 0.03634 ( 792) hydrogen bonds : angle 5.11286 ( 2196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 521 time to evaluate : 0.805 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: U 376 ASP cc_start: 0.6564 (t0) cc_final: 0.6255 (t0) REVERT: U 584 LYS cc_start: 0.7636 (tmmt) cc_final: 0.7029 (tmmt) REVERT: U 585 GLU cc_start: 0.7669 (tp30) cc_final: 0.7453 (tp30) REVERT: U 588 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.7088 (mtt-85) REVERT: U 644 LYS cc_start: 0.8314 (mttp) cc_final: 0.7879 (mtpt) REVERT: U 754 GLU cc_start: 0.7273 (mp0) cc_final: 0.7030 (mp0) REVERT: U 774 ILE cc_start: 0.7951 (mm) cc_final: 0.7584 (pt) REVERT: U 897 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7998 (mp) REVERT: U 1091 ILE cc_start: 0.7753 (mm) cc_final: 0.7348 (pp) REVERT: Q 44 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8079 (mtm-85) REVERT: Q 119 ASP cc_start: 0.7899 (t70) cc_final: 0.7657 (t0) REVERT: Q 172 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8281 (p0) REVERT: Q 265 MET cc_start: 0.8095 (ttp) cc_final: 0.7763 (ttt) REVERT: Q 287 LYS cc_start: 0.7167 (tptt) cc_final: 0.6941 (mptt) REVERT: Q 359 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7845 (mmtp) REVERT: Q 363 TYR cc_start: 0.8320 (m-80) cc_final: 0.8004 (m-80) REVERT: Q 478 SER cc_start: 0.8067 (m) cc_final: 0.7458 (p) REVERT: Q 509 GLU cc_start: 0.7283 (tt0) cc_final: 0.7044 (tt0) REVERT: W 195 LEU cc_start: 0.6787 (tp) cc_final: 0.6079 (mp) REVERT: W 235 MET cc_start: 0.7163 (tpp) cc_final: 0.6890 (tpp) REVERT: W 267 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6914 (mp-120) REVERT: W 269 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7155 (mtm-85) REVERT: W 286 THR cc_start: 0.7842 (p) cc_final: 0.7590 (m) REVERT: W 287 ASP cc_start: 0.6985 (t70) cc_final: 0.6593 (t0) REVERT: W 389 GLN cc_start: 0.8040 (tp40) cc_final: 0.7757 (tp40) REVERT: W 489 GLU cc_start: 0.7609 (mp0) cc_final: 0.7286 (mp0) REVERT: W 856 ILE cc_start: 0.8340 (pt) cc_final: 0.8040 (mt) REVERT: W 901 ASP cc_start: 0.6875 (m-30) cc_final: 0.6546 (m-30) REVERT: W 1367 TYR cc_start: 0.7390 (p90) cc_final: 0.7141 (p90) REVERT: W 1471 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7323 (m110) REVERT: W 1575 MET cc_start: 0.5971 (mtp) cc_final: 0.5609 (mtp) REVERT: S 17 SER cc_start: 0.8021 (t) cc_final: 0.7800 (t) REVERT: S 65 TYR cc_start: 0.8631 (t80) cc_final: 0.8235 (t80) REVERT: S 85 ASN cc_start: 0.7442 (t0) cc_final: 0.7130 (t0) REVERT: S 124 LEU cc_start: 0.8397 (tt) cc_final: 0.8110 (tp) REVERT: S 301 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8106 (mmmm) REVERT: S 307 ASP cc_start: 0.7927 (p0) cc_final: 0.7690 (p0) REVERT: S 571 GLU cc_start: 0.7400 (mp0) cc_final: 0.6944 (mp0) outliers start: 54 outliers final: 19 residues processed: 537 average time/residue: 0.5987 time to fit residues: 364.2160 Evaluate side-chains 520 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 497 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 798 ASP Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 945 GLN Chi-restraints excluded: chain U residue 966 MET Chi-restraints excluded: chain Q residue 172 ASN Chi-restraints excluded: chain Q residue 305 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain W residue 267 GLN Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 849 VAL Chi-restraints excluded: chain W residue 1039 ASP Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain W residue 1471 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 446 SER Chi-restraints excluded: chain S residue 490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 123 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 921 GLN Q 163 GLN Q 269 ASN W 255 ASN W 350 ASN W 916 ASN W 981 ASN W1056 GLN W1059 GLN W1154 ASN W1471 ASN S 121 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.133887 restraints weight = 28732.735| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.95 r_work: 0.3693 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20270 Z= 0.210 Angle : 0.566 8.433 27439 Z= 0.293 Chirality : 0.047 0.174 3021 Planarity : 0.005 0.050 3474 Dihedral : 4.484 36.044 2610 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.02 % Allowed : 16.41 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.17), residues: 2353 helix: 0.59 (0.19), residues: 796 sheet: -0.15 (0.23), residues: 520 loop : -0.81 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 188 TYR 0.020 0.002 TYR Q 48 PHE 0.028 0.002 PHE S 610 TRP 0.017 0.002 TRP Q 338 HIS 0.005 0.001 HIS W1427 Details of bonding type rmsd covalent geometry : bond 0.00500 (20270) covalent geometry : angle 0.56552 (27439) hydrogen bonds : bond 0.03935 ( 792) hydrogen bonds : angle 5.05800 ( 2196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 507 time to evaluate : 0.763 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: U 376 ASP cc_start: 0.6535 (t0) cc_final: 0.6244 (t0) REVERT: U 577 SER cc_start: 0.7710 (m) cc_final: 0.7454 (p) REVERT: U 584 LYS cc_start: 0.7656 (tmmt) cc_final: 0.7115 (tmmt) REVERT: U 588 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.7143 (mtt-85) REVERT: U 644 LYS cc_start: 0.8336 (mttp) cc_final: 0.7888 (mtpt) REVERT: U 754 GLU cc_start: 0.7316 (mp0) cc_final: 0.7043 (mp0) REVERT: U 774 ILE cc_start: 0.7980 (mm) cc_final: 0.7652 (pt) REVERT: U 817 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7231 (mt-10) REVERT: U 845 THR cc_start: 0.8351 (t) cc_final: 0.7929 (m) REVERT: U 897 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8009 (mp) REVERT: U 1091 ILE cc_start: 0.7831 (mm) cc_final: 0.7412 (pp) REVERT: Q 20 SER cc_start: 0.8412 (t) cc_final: 0.8142 (p) REVERT: Q 44 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8067 (mtm-85) REVERT: Q 119 ASP cc_start: 0.7920 (t70) cc_final: 0.7695 (t0) REVERT: Q 269 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7383 (t0) REVERT: Q 287 LYS cc_start: 0.7228 (tptt) cc_final: 0.6949 (mptt) REVERT: Q 323 GLU cc_start: 0.7568 (tt0) cc_final: 0.7361 (mt-10) REVERT: Q 363 TYR cc_start: 0.8353 (m-80) cc_final: 0.8034 (m-80) REVERT: Q 478 SER cc_start: 0.8100 (m) cc_final: 0.7535 (p) REVERT: W 195 LEU cc_start: 0.6830 (tp) cc_final: 0.6094 (mp) REVERT: W 267 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7096 (mp10) REVERT: W 269 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7175 (mtm-85) REVERT: W 287 ASP cc_start: 0.7032 (t70) cc_final: 0.6658 (t0) REVERT: W 292 PHE cc_start: 0.8076 (m-80) cc_final: 0.7802 (m-80) REVERT: W 389 GLN cc_start: 0.8049 (tp40) cc_final: 0.7774 (tp40) REVERT: W 470 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8069 (mt) REVERT: W 489 GLU cc_start: 0.7614 (mp0) cc_final: 0.7301 (mp0) REVERT: W 856 ILE cc_start: 0.8382 (pt) cc_final: 0.8072 (mt) REVERT: W 1367 TYR cc_start: 0.7412 (p90) cc_final: 0.7157 (p90) REVERT: W 1471 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7539 (m110) REVERT: W 1495 PHE cc_start: 0.7551 (m-80) cc_final: 0.7322 (m-80) REVERT: W 1575 MET cc_start: 0.6031 (mtp) cc_final: 0.5660 (mtp) REVERT: S 17 SER cc_start: 0.8007 (t) cc_final: 0.7781 (t) REVERT: S 65 TYR cc_start: 0.8634 (t80) cc_final: 0.8243 (t80) REVERT: S 85 ASN cc_start: 0.7455 (t0) cc_final: 0.7135 (t0) REVERT: S 124 LEU cc_start: 0.8400 (tt) cc_final: 0.8155 (tp) REVERT: S 301 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8093 (mmmm) REVERT: S 344 SER cc_start: 0.8601 (t) cc_final: 0.8230 (p) REVERT: S 571 GLU cc_start: 0.7453 (mp0) cc_final: 0.7036 (mp0) outliers start: 68 outliers final: 34 residues processed: 534 average time/residue: 0.5901 time to fit residues: 356.5697 Evaluate side-chains 538 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 500 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 25 ILE Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 667 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 798 ASP Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 945 GLN Chi-restraints excluded: chain U residue 966 MET Chi-restraints excluded: chain U residue 1129 LEU Chi-restraints excluded: chain Q residue 269 ASN Chi-restraints excluded: chain Q residue 305 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 412 MET Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 506 LYS Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 849 VAL Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 928 TYR Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1011 LEU Chi-restraints excluded: chain W residue 1117 ILE Chi-restraints excluded: chain W residue 1348 VAL Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain W residue 1471 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 264 MET Chi-restraints excluded: chain S residue 443 ARG Chi-restraints excluded: chain S residue 446 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 221 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 136 optimal weight: 0.0980 chunk 78 optimal weight: 0.0870 chunk 123 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 921 GLN Q 163 GLN W 267 GLN W 350 ASN W 916 ASN W 981 ASN W1056 GLN W1059 GLN W1154 ASN W1471 ASN S 121 GLN S 206 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134218 restraints weight = 28745.720| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.91 r_work: 0.3701 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20270 Z= 0.192 Angle : 0.564 8.345 27439 Z= 0.291 Chirality : 0.047 0.218 3021 Planarity : 0.004 0.050 3474 Dihedral : 4.482 34.871 2610 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.16 % Allowed : 17.04 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.30 (0.17), residues: 2353 helix: 0.63 (0.19), residues: 795 sheet: -0.15 (0.23), residues: 523 loop : -0.80 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 519 TYR 0.021 0.001 TYR W1497 PHE 0.029 0.002 PHE S 610 TRP 0.017 0.001 TRP Q 338 HIS 0.004 0.001 HIS W1427 Details of bonding type rmsd covalent geometry : bond 0.00458 (20270) covalent geometry : angle 0.56430 (27439) hydrogen bonds : bond 0.03774 ( 792) hydrogen bonds : angle 5.02120 ( 2196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 507 time to evaluate : 0.667 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: U 376 ASP cc_start: 0.6567 (t0) cc_final: 0.6257 (t0) REVERT: U 577 SER cc_start: 0.7675 (m) cc_final: 0.7433 (p) REVERT: U 584 LYS cc_start: 0.7692 (tmmt) cc_final: 0.7158 (tmmt) REVERT: U 588 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.7112 (mtt-85) REVERT: U 644 LYS cc_start: 0.8374 (mttp) cc_final: 0.7925 (mtpt) REVERT: U 754 GLU cc_start: 0.7291 (mp0) cc_final: 0.7016 (mp0) REVERT: U 774 ILE cc_start: 0.7974 (mm) cc_final: 0.7659 (pt) REVERT: U 817 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7257 (mt-10) REVERT: U 845 THR cc_start: 0.8338 (t) cc_final: 0.7919 (m) REVERT: U 897 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8014 (mp) REVERT: U 1091 ILE cc_start: 0.7830 (mm) cc_final: 0.7434 (pp) REVERT: Q 20 SER cc_start: 0.8413 (t) cc_final: 0.8169 (p) REVERT: Q 44 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.8040 (mtm-85) REVERT: Q 119 ASP cc_start: 0.7901 (t70) cc_final: 0.7676 (t0) REVERT: Q 287 LYS cc_start: 0.7194 (tptt) cc_final: 0.6959 (mptt) REVERT: Q 363 TYR cc_start: 0.8331 (m-80) cc_final: 0.8013 (m-80) REVERT: Q 478 SER cc_start: 0.8110 (m) cc_final: 0.7558 (p) REVERT: W 124 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6678 (tp30) REVERT: W 195 LEU cc_start: 0.6738 (tp) cc_final: 0.6009 (mp) REVERT: W 269 ARG cc_start: 0.7304 (mtm180) cc_final: 0.7088 (mtm-85) REVERT: W 287 ASP cc_start: 0.6942 (t70) cc_final: 0.6582 (t0) REVERT: W 389 GLN cc_start: 0.8018 (tp40) cc_final: 0.7758 (tp40) REVERT: W 470 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8106 (mt) REVERT: W 489 GLU cc_start: 0.7601 (mp0) cc_final: 0.7371 (mp0) REVERT: W 855 SER cc_start: 0.7894 (m) cc_final: 0.7567 (m) REVERT: W 856 ILE cc_start: 0.8372 (pt) cc_final: 0.8081 (mt) REVERT: W 1041 MET cc_start: 0.7385 (mpp) cc_final: 0.7065 (mtt) REVERT: W 1367 TYR cc_start: 0.7425 (p90) cc_final: 0.7194 (p90) REVERT: W 1471 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7379 (m-40) REVERT: W 1495 PHE cc_start: 0.7464 (m-80) cc_final: 0.7215 (m-80) REVERT: W 1575 MET cc_start: 0.5990 (mtp) cc_final: 0.5623 (mtp) REVERT: S 17 SER cc_start: 0.8001 (t) cc_final: 0.7785 (t) REVERT: S 65 TYR cc_start: 0.8619 (t80) cc_final: 0.8255 (t80) REVERT: S 85 ASN cc_start: 0.7399 (t0) cc_final: 0.7097 (t0) REVERT: S 124 LEU cc_start: 0.8380 (tt) cc_final: 0.8116 (tp) REVERT: S 301 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8084 (mmmm) REVERT: S 344 SER cc_start: 0.8624 (t) cc_final: 0.8286 (p) REVERT: S 460 MET cc_start: 0.7112 (mmm) cc_final: 0.6909 (mmm) REVERT: S 571 GLU cc_start: 0.7417 (mp0) cc_final: 0.7005 (mp0) outliers start: 71 outliers final: 42 residues processed: 538 average time/residue: 0.5797 time to fit residues: 354.6393 Evaluate side-chains 543 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 498 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 25 ILE Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 572 THR Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 652 ILE Chi-restraints excluded: chain U residue 667 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 901 LYS Chi-restraints excluded: chain U residue 966 MET Chi-restraints excluded: chain U residue 1129 LEU Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 343 SER Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 412 MET Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 506 LYS Chi-restraints excluded: chain Q residue 512 SER Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 460 LEU Chi-restraints excluded: chain W residue 462 SER Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 501 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 849 VAL Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1011 LEU Chi-restraints excluded: chain W residue 1021 GLN Chi-restraints excluded: chain W residue 1022 VAL Chi-restraints excluded: chain W residue 1348 VAL Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain W residue 1471 ASN Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 264 MET Chi-restraints excluded: chain S residue 267 VAL Chi-restraints excluded: chain S residue 443 ARG Chi-restraints excluded: chain S residue 446 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 61 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 921 GLN Q 97 ASN Q 111 HIS Q 163 GLN W 267 GLN W 350 ASN W 493 HIS W 916 ASN W 981 ASN W1056 GLN W1154 ASN W1345 ASN W1471 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.152155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134279 restraints weight = 28589.813| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.91 r_work: 0.3701 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20270 Z= 0.187 Angle : 0.568 14.642 27439 Z= 0.292 Chirality : 0.047 0.186 3021 Planarity : 0.004 0.046 3474 Dihedral : 4.478 33.701 2610 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.43 % Allowed : 18.37 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.29 (0.17), residues: 2353 helix: 0.67 (0.19), residues: 789 sheet: -0.23 (0.22), residues: 533 loop : -0.76 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 519 TYR 0.024 0.001 TYR W1507 PHE 0.029 0.002 PHE S 610 TRP 0.017 0.001 TRP Q 338 HIS 0.004 0.001 HIS W 322 Details of bonding type rmsd covalent geometry : bond 0.00446 (20270) covalent geometry : angle 0.56762 (27439) hydrogen bonds : bond 0.03740 ( 792) hydrogen bonds : angle 4.99162 ( 2196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 510 time to evaluate : 0.865 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: U 376 ASP cc_start: 0.6557 (t0) cc_final: 0.6244 (t0) REVERT: U 577 SER cc_start: 0.7657 (m) cc_final: 0.7401 (p) REVERT: U 584 LYS cc_start: 0.7676 (tmmt) cc_final: 0.7126 (tmmt) REVERT: U 588 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.7099 (mtt-85) REVERT: U 644 LYS cc_start: 0.8396 (mttp) cc_final: 0.7965 (mtpt) REVERT: U 754 GLU cc_start: 0.7309 (mp0) cc_final: 0.7028 (mp0) REVERT: U 774 ILE cc_start: 0.7975 (mm) cc_final: 0.7647 (pt) REVERT: U 817 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7285 (mt-10) REVERT: U 897 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7989 (mp) REVERT: U 1091 ILE cc_start: 0.7823 (mm) cc_final: 0.7419 (pp) REVERT: Q 20 SER cc_start: 0.8408 (t) cc_final: 0.8153 (p) REVERT: Q 44 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.8048 (mtm-85) REVERT: Q 119 ASP cc_start: 0.7917 (t70) cc_final: 0.7680 (t0) REVERT: Q 237 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6734 (mm-30) REVERT: Q 287 LYS cc_start: 0.7227 (tptt) cc_final: 0.6983 (mptt) REVERT: Q 363 TYR cc_start: 0.8326 (m-80) cc_final: 0.7996 (m-80) REVERT: Q 478 SER cc_start: 0.8111 (m) cc_final: 0.7551 (p) REVERT: W 124 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6702 (tp30) REVERT: W 195 LEU cc_start: 0.6723 (tp) cc_final: 0.5983 (mp) REVERT: W 269 ARG cc_start: 0.7334 (mtm180) cc_final: 0.7103 (mtm-85) REVERT: W 286 THR cc_start: 0.7886 (p) cc_final: 0.7681 (m) REVERT: W 287 ASP cc_start: 0.6929 (t70) cc_final: 0.6558 (t0) REVERT: W 301 GLN cc_start: 0.8125 (mt0) cc_final: 0.7897 (mt0) REVERT: W 389 GLN cc_start: 0.8019 (tp40) cc_final: 0.7769 (tp40) REVERT: W 470 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8117 (mt) REVERT: W 489 GLU cc_start: 0.7614 (mp0) cc_final: 0.7379 (mp0) REVERT: W 855 SER cc_start: 0.7892 (m) cc_final: 0.7572 (m) REVERT: W 856 ILE cc_start: 0.8356 (pt) cc_final: 0.8065 (mt) REVERT: W 905 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7060 (tmtt) REVERT: W 1367 TYR cc_start: 0.7418 (p90) cc_final: 0.7203 (p90) REVERT: W 1495 PHE cc_start: 0.7505 (m-80) cc_final: 0.7242 (m-80) REVERT: W 1575 MET cc_start: 0.6046 (mtp) cc_final: 0.5666 (mtp) REVERT: S 17 SER cc_start: 0.8003 (t) cc_final: 0.7790 (t) REVERT: S 65 TYR cc_start: 0.8628 (t80) cc_final: 0.8274 (t80) REVERT: S 85 ASN cc_start: 0.7395 (t0) cc_final: 0.7064 (t0) REVERT: S 124 LEU cc_start: 0.8358 (tt) cc_final: 0.8106 (tp) REVERT: S 220 GLU cc_start: 0.7816 (mp0) cc_final: 0.7614 (mt-10) REVERT: S 239 VAL cc_start: 0.8275 (p) cc_final: 0.8012 (m) REVERT: S 301 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8080 (mmmm) REVERT: S 344 SER cc_start: 0.8608 (t) cc_final: 0.8262 (p) REVERT: S 460 MET cc_start: 0.7120 (mmm) cc_final: 0.6895 (mmm) REVERT: S 571 GLU cc_start: 0.7438 (mp0) cc_final: 0.7030 (mp0) REVERT: S 572 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6485 (mm-30) outliers start: 77 outliers final: 47 residues processed: 547 average time/residue: 0.5719 time to fit residues: 356.8240 Evaluate side-chains 544 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 494 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 25 ILE Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 572 THR Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 652 ILE Chi-restraints excluded: chain U residue 667 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 901 LYS Chi-restraints excluded: chain U residue 1129 LEU Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 134 SER Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 202 SER Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 343 SER Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 506 LYS Chi-restraints excluded: chain Q residue 512 SER Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain W residue 462 SER Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 501 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 849 VAL Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1021 GLN Chi-restraints excluded: chain W residue 1022 VAL Chi-restraints excluded: chain W residue 1035 SER Chi-restraints excluded: chain W residue 1348 VAL Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain S residue 264 MET Chi-restraints excluded: chain S residue 267 VAL Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 443 ARG Chi-restraints excluded: chain S residue 446 SER Chi-restraints excluded: chain S residue 572 GLU Chi-restraints excluded: chain S residue 595 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 214 optimal weight: 0.3980 chunk 63 optimal weight: 0.0060 chunk 148 optimal weight: 0.0370 chunk 228 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 833 HIS U 921 GLN Q 163 GLN Q 205 ASN W 267 GLN W 350 ASN W 916 ASN W 981 ASN W1056 GLN W1154 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.135120 restraints weight = 28833.669| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.92 r_work: 0.3715 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20270 Z= 0.141 Angle : 0.550 10.967 27439 Z= 0.282 Chirality : 0.045 0.169 3021 Planarity : 0.004 0.048 3474 Dihedral : 4.382 32.120 2610 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.98 % Allowed : 19.17 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.22 (0.17), residues: 2353 helix: 0.79 (0.19), residues: 788 sheet: -0.28 (0.22), residues: 538 loop : -0.72 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 519 TYR 0.030 0.001 TYR W1507 PHE 0.029 0.001 PHE S 610 TRP 0.016 0.001 TRP Q 338 HIS 0.004 0.001 HIS W 322 Details of bonding type rmsd covalent geometry : bond 0.00335 (20270) covalent geometry : angle 0.55007 (27439) hydrogen bonds : bond 0.03486 ( 792) hydrogen bonds : angle 4.88194 ( 2196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 513 time to evaluate : 0.816 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: U 376 ASP cc_start: 0.6559 (t0) cc_final: 0.6247 (t0) REVERT: U 577 SER cc_start: 0.7668 (m) cc_final: 0.7422 (p) REVERT: U 584 LYS cc_start: 0.7709 (tmmt) cc_final: 0.7168 (tmmt) REVERT: U 588 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.7090 (mtt-85) REVERT: U 644 LYS cc_start: 0.8410 (mttp) cc_final: 0.8001 (mtpt) REVERT: U 754 GLU cc_start: 0.7281 (mp0) cc_final: 0.7026 (mp0) REVERT: U 774 ILE cc_start: 0.7965 (mm) cc_final: 0.7633 (pt) REVERT: U 817 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7284 (mt-10) REVERT: U 897 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8035 (mp) REVERT: U 931 GLU cc_start: 0.7129 (mp0) cc_final: 0.6765 (mp0) REVERT: U 1091 ILE cc_start: 0.7775 (mm) cc_final: 0.7354 (pp) REVERT: Q 20 SER cc_start: 0.8386 (t) cc_final: 0.8163 (p) REVERT: Q 44 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: Q 101 SER cc_start: 0.8680 (t) cc_final: 0.8410 (p) REVERT: Q 119 ASP cc_start: 0.7881 (t70) cc_final: 0.7655 (t0) REVERT: Q 287 LYS cc_start: 0.7209 (tptt) cc_final: 0.6981 (mptt) REVERT: Q 363 TYR cc_start: 0.8304 (m-80) cc_final: 0.7974 (m-80) REVERT: Q 478 SER cc_start: 0.8073 (m) cc_final: 0.7518 (p) REVERT: W 124 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6689 (tp30) REVERT: W 195 LEU cc_start: 0.6689 (tp) cc_final: 0.5973 (mp) REVERT: W 267 GLN cc_start: 0.7360 (mm110) cc_final: 0.6988 (mp-120) REVERT: W 269 ARG cc_start: 0.7298 (mtm180) cc_final: 0.7084 (mtm-85) REVERT: W 286 THR cc_start: 0.7875 (p) cc_final: 0.7654 (m) REVERT: W 287 ASP cc_start: 0.6880 (t70) cc_final: 0.6520 (t0) REVERT: W 389 GLN cc_start: 0.8014 (tp40) cc_final: 0.7751 (tp40) REVERT: W 470 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8128 (mt) REVERT: W 489 GLU cc_start: 0.7619 (mp0) cc_final: 0.7387 (mp0) REVERT: W 855 SER cc_start: 0.7874 (m) cc_final: 0.7566 (m) REVERT: W 856 ILE cc_start: 0.8311 (pt) cc_final: 0.8058 (mt) REVERT: W 943 ARG cc_start: 0.7953 (mpt180) cc_final: 0.6912 (mpt180) REVERT: W 1495 PHE cc_start: 0.7419 (m-80) cc_final: 0.7198 (m-80) REVERT: W 1575 MET cc_start: 0.6003 (mtp) cc_final: 0.5632 (mtp) REVERT: S 17 SER cc_start: 0.7994 (t) cc_final: 0.7786 (t) REVERT: S 65 TYR cc_start: 0.8618 (t80) cc_final: 0.8283 (t80) REVERT: S 85 ASN cc_start: 0.7390 (t0) cc_final: 0.7089 (t0) REVERT: S 124 LEU cc_start: 0.8343 (tt) cc_final: 0.8053 (tp) REVERT: S 239 VAL cc_start: 0.8269 (p) cc_final: 0.8005 (m) REVERT: S 301 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8054 (mmmm) REVERT: S 344 SER cc_start: 0.8610 (t) cc_final: 0.8280 (p) REVERT: S 460 MET cc_start: 0.7128 (mmm) cc_final: 0.6918 (mmm) REVERT: S 571 GLU cc_start: 0.7427 (mp0) cc_final: 0.7032 (mp0) outliers start: 67 outliers final: 45 residues processed: 542 average time/residue: 0.5912 time to fit residues: 364.3650 Evaluate side-chains 552 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 505 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 572 THR Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 667 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 949 VAL Chi-restraints excluded: chain U residue 1113 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 134 SER Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 202 SER Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 343 SER Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 512 SER Chi-restraints excluded: chain Q residue 533 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 462 SER Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 473 SER Chi-restraints excluded: chain W residue 501 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1021 GLN Chi-restraints excluded: chain W residue 1022 VAL Chi-restraints excluded: chain W residue 1117 ILE Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 236 THR Chi-restraints excluded: chain S residue 267 VAL Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 443 ARG Chi-restraints excluded: chain S residue 446 SER Chi-restraints excluded: chain S residue 595 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 170 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 134 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN U 611 GLN U 921 GLN ** Q 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 GLN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 350 ASN W 916 ASN W 981 ASN W1056 GLN W1059 GLN W1154 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134388 restraints weight = 28486.773| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.91 r_work: 0.3700 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20270 Z= 0.196 Angle : 0.591 10.264 27439 Z= 0.303 Chirality : 0.047 0.185 3021 Planarity : 0.004 0.047 3474 Dihedral : 4.490 32.010 2610 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.80 % Allowed : 19.97 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.25 (0.17), residues: 2353 helix: 0.76 (0.19), residues: 790 sheet: -0.25 (0.22), residues: 529 loop : -0.75 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 443 TYR 0.040 0.002 TYR W1497 PHE 0.032 0.002 PHE Q 108 TRP 0.016 0.002 TRP W1414 HIS 0.005 0.001 HIS U 14 Details of bonding type rmsd covalent geometry : bond 0.00468 (20270) covalent geometry : angle 0.59120 (27439) hydrogen bonds : bond 0.03787 ( 792) hydrogen bonds : angle 4.95378 ( 2196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 509 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 376 ASP cc_start: 0.6601 (t0) cc_final: 0.6290 (t0) REVERT: U 577 SER cc_start: 0.7645 (m) cc_final: 0.7389 (p) REVERT: U 584 LYS cc_start: 0.7704 (tmmt) cc_final: 0.7155 (tmmt) REVERT: U 588 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7096 (mtt-85) REVERT: U 644 LYS cc_start: 0.8424 (mttp) cc_final: 0.7987 (mtpt) REVERT: U 754 GLU cc_start: 0.7299 (mp0) cc_final: 0.7037 (mp0) REVERT: U 774 ILE cc_start: 0.7972 (mm) cc_final: 0.7639 (pt) REVERT: U 817 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7288 (mt-10) REVERT: U 897 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8004 (mp) REVERT: U 1091 ILE cc_start: 0.7840 (mm) cc_final: 0.7435 (pp) REVERT: U 1105 LEU cc_start: 0.8699 (mp) cc_final: 0.8487 (mp) REVERT: U 1112 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7953 (mtmm) REVERT: Q 20 SER cc_start: 0.8398 (t) cc_final: 0.8132 (p) REVERT: Q 44 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: Q 101 SER cc_start: 0.8711 (t) cc_final: 0.8447 (p) REVERT: Q 119 ASP cc_start: 0.7927 (t70) cc_final: 0.7683 (t0) REVERT: Q 237 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6731 (mm-30) REVERT: Q 287 LYS cc_start: 0.7247 (tptt) cc_final: 0.6978 (mptt) REVERT: Q 363 TYR cc_start: 0.8321 (m-80) cc_final: 0.7986 (m-80) REVERT: Q 478 SER cc_start: 0.8102 (m) cc_final: 0.7526 (p) REVERT: Q 533 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7694 (mp) REVERT: W 124 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6739 (tp30) REVERT: W 195 LEU cc_start: 0.6746 (tp) cc_final: 0.6012 (mp) REVERT: W 269 ARG cc_start: 0.7347 (mtm180) cc_final: 0.7138 (mtm-85) REVERT: W 287 ASP cc_start: 0.6925 (t70) cc_final: 0.6563 (t0) REVERT: W 301 GLN cc_start: 0.8124 (mt0) cc_final: 0.7913 (mt0) REVERT: W 389 GLN cc_start: 0.7996 (tp40) cc_final: 0.7748 (tp40) REVERT: W 470 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8127 (mt) REVERT: W 489 GLU cc_start: 0.7638 (mp0) cc_final: 0.7401 (mp0) REVERT: W 855 SER cc_start: 0.7864 (m) cc_final: 0.7567 (m) REVERT: W 856 ILE cc_start: 0.8335 (pt) cc_final: 0.8070 (mt) REVERT: W 905 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6934 (tmtt) REVERT: W 1463 LYS cc_start: 0.8257 (mmmt) cc_final: 0.8001 (tppt) REVERT: W 1495 PHE cc_start: 0.7413 (m-80) cc_final: 0.7180 (m-80) REVERT: W 1575 MET cc_start: 0.6079 (mtp) cc_final: 0.5700 (mtp) REVERT: S 17 SER cc_start: 0.8015 (t) cc_final: 0.7802 (t) REVERT: S 65 TYR cc_start: 0.8633 (t80) cc_final: 0.8287 (t80) REVERT: S 85 ASN cc_start: 0.7395 (t0) cc_final: 0.7077 (t0) REVERT: S 124 LEU cc_start: 0.8359 (tt) cc_final: 0.8121 (tp) REVERT: S 239 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8013 (m) REVERT: S 301 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8080 (mmmm) REVERT: S 344 SER cc_start: 0.8625 (t) cc_final: 0.8285 (p) REVERT: S 460 MET cc_start: 0.7163 (mmm) cc_final: 0.6941 (mmm) REVERT: S 571 GLU cc_start: 0.7438 (mp0) cc_final: 0.7016 (mp0) outliers start: 63 outliers final: 44 residues processed: 537 average time/residue: 0.5881 time to fit residues: 358.5225 Evaluate side-chains 548 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 500 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 572 THR Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 667 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 1113 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 202 SER Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 343 SER Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 512 SER Chi-restraints excluded: chain Q residue 533 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 473 SER Chi-restraints excluded: chain W residue 501 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 549 LYS Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1021 GLN Chi-restraints excluded: chain W residue 1022 VAL Chi-restraints excluded: chain W residue 1035 SER Chi-restraints excluded: chain W residue 1117 ILE Chi-restraints excluded: chain W residue 1348 VAL Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain S residue 236 THR Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 267 VAL Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 443 ARG Chi-restraints excluded: chain S residue 446 SER Chi-restraints excluded: chain S residue 595 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 137 optimal weight: 0.4980 chunk 214 optimal weight: 0.3980 chunk 228 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 921 GLN Q 90 ASN ** Q 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 GLN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 267 GLN W 350 ASN W 916 ASN W 981 ASN W1056 GLN W1154 ASN W1471 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.151445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.133508 restraints weight = 28517.573| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.91 r_work: 0.3691 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20270 Z= 0.237 Angle : 0.619 10.483 27439 Z= 0.319 Chirality : 0.049 0.217 3021 Planarity : 0.004 0.048 3474 Dihedral : 4.635 31.636 2610 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.67 % Allowed : 20.69 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.32 (0.17), residues: 2353 helix: 0.67 (0.19), residues: 790 sheet: -0.24 (0.22), residues: 523 loop : -0.80 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 443 TYR 0.033 0.002 TYR W1507 PHE 0.031 0.002 PHE S 610 TRP 0.021 0.002 TRP W1414 HIS 0.006 0.001 HIS U 14 Details of bonding type rmsd covalent geometry : bond 0.00566 (20270) covalent geometry : angle 0.61861 (27439) hydrogen bonds : bond 0.04001 ( 792) hydrogen bonds : angle 5.03916 ( 2196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 501 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 368 MET cc_start: 0.6707 (mmm) cc_final: 0.6298 (mmm) REVERT: U 376 ASP cc_start: 0.6620 (t0) cc_final: 0.6317 (t0) REVERT: U 577 SER cc_start: 0.7658 (m) cc_final: 0.7393 (p) REVERT: U 584 LYS cc_start: 0.7717 (tmmt) cc_final: 0.7167 (tmmt) REVERT: U 588 ARG cc_start: 0.7519 (ttt-90) cc_final: 0.7119 (mtt-85) REVERT: U 644 LYS cc_start: 0.8428 (mttp) cc_final: 0.7978 (mtpt) REVERT: U 754 GLU cc_start: 0.7327 (mp0) cc_final: 0.7007 (mp0) REVERT: U 774 ILE cc_start: 0.7985 (mm) cc_final: 0.7663 (pt) REVERT: U 817 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7280 (mt-10) REVERT: U 897 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7998 (mp) REVERT: U 1091 ILE cc_start: 0.7893 (mm) cc_final: 0.7631 (pp) REVERT: U 1105 LEU cc_start: 0.8724 (mp) cc_final: 0.8493 (mp) REVERT: U 1112 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7857 (mtmm) REVERT: Q 20 SER cc_start: 0.8408 (t) cc_final: 0.8170 (p) REVERT: Q 44 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8041 (mtm-85) REVERT: Q 101 SER cc_start: 0.8702 (t) cc_final: 0.8417 (p) REVERT: Q 119 ASP cc_start: 0.7940 (t70) cc_final: 0.7711 (t0) REVERT: Q 287 LYS cc_start: 0.7247 (tptt) cc_final: 0.6979 (mptt) REVERT: Q 363 TYR cc_start: 0.8348 (m-80) cc_final: 0.8008 (m-80) REVERT: Q 478 SER cc_start: 0.8156 (m) cc_final: 0.7567 (p) REVERT: Q 533 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7714 (mp) REVERT: W 179 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4657 (tt) REVERT: W 195 LEU cc_start: 0.6754 (tp) cc_final: 0.5995 (mp) REVERT: W 267 GLN cc_start: 0.7340 (mm110) cc_final: 0.6955 (mp-120) REVERT: W 287 ASP cc_start: 0.6885 (t70) cc_final: 0.6560 (t0) REVERT: W 301 GLN cc_start: 0.8126 (mt0) cc_final: 0.7893 (mt0) REVERT: W 389 GLN cc_start: 0.8001 (tp40) cc_final: 0.7765 (tp40) REVERT: W 470 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8128 (mt) REVERT: W 489 GLU cc_start: 0.7631 (mp0) cc_final: 0.7389 (mp0) REVERT: W 855 SER cc_start: 0.7883 (m) cc_final: 0.7647 (m) REVERT: W 856 ILE cc_start: 0.8385 (pt) cc_final: 0.8124 (mt) REVERT: W 905 LYS cc_start: 0.7360 (mmmt) cc_final: 0.6907 (tmtt) REVERT: W 909 ASP cc_start: 0.7501 (m-30) cc_final: 0.7160 (m-30) REVERT: W 1463 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7991 (tppt) REVERT: W 1495 PHE cc_start: 0.7457 (m-80) cc_final: 0.7212 (m-80) REVERT: W 1575 MET cc_start: 0.6096 (mtp) cc_final: 0.5714 (mtp) REVERT: S 17 SER cc_start: 0.8006 (t) cc_final: 0.7800 (t) REVERT: S 65 TYR cc_start: 0.8638 (t80) cc_final: 0.8295 (t80) REVERT: S 85 ASN cc_start: 0.7387 (t0) cc_final: 0.7055 (t0) REVERT: S 124 LEU cc_start: 0.8373 (tt) cc_final: 0.8147 (tp) REVERT: S 239 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8009 (m) REVERT: S 301 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8176 (mmmm) REVERT: S 460 MET cc_start: 0.7170 (mmm) cc_final: 0.6934 (mmm) REVERT: S 571 GLU cc_start: 0.7434 (mp0) cc_final: 0.7024 (mp0) outliers start: 60 outliers final: 45 residues processed: 529 average time/residue: 0.5773 time to fit residues: 348.1993 Evaluate side-chains 543 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 493 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 544 ILE Chi-restraints excluded: chain U residue 572 THR Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 667 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 949 VAL Chi-restraints excluded: chain U residue 1113 VAL Chi-restraints excluded: chain U residue 1141 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 202 SER Chi-restraints excluded: chain Q residue 218 MET Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 343 SER Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 451 VAL Chi-restraints excluded: chain Q residue 512 SER Chi-restraints excluded: chain Q residue 533 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 404 VAL Chi-restraints excluded: chain W residue 440 SER Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 473 SER Chi-restraints excluded: chain W residue 501 SER Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 549 LYS Chi-restraints excluded: chain W residue 874 VAL Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1021 GLN Chi-restraints excluded: chain W residue 1022 VAL Chi-restraints excluded: chain W residue 1035 SER Chi-restraints excluded: chain W residue 1117 ILE Chi-restraints excluded: chain W residue 1348 VAL Chi-restraints excluded: chain W residue 1391 ILE Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 267 VAL Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 446 SER Chi-restraints excluded: chain S residue 595 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0980 chunk 53 optimal weight: 0.1980 chunk 198 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 161 optimal weight: 0.2980 chunk 215 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 74 optimal weight: 0.0060 chunk 80 optimal weight: 0.9980 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN U 921 GLN Q 90 ASN ** Q 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 GLN ** Q 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 350 ASN W 916 ASN W 981 ASN W1059 GLN W1154 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136689 restraints weight = 28830.690| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.93 r_work: 0.3738 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20270 Z= 0.111 Angle : 0.560 8.280 27439 Z= 0.287 Chirality : 0.045 0.181 3021 Planarity : 0.004 0.049 3474 Dihedral : 4.401 29.505 2610 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.82 % Allowed : 21.93 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.12 (0.17), residues: 2353 helix: 0.87 (0.19), residues: 789 sheet: -0.19 (0.22), residues: 531 loop : -0.68 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 443 TYR 0.027 0.001 TYR W1507 PHE 0.026 0.001 PHE S 610 TRP 0.025 0.001 TRP Q 229 HIS 0.009 0.001 HIS W 917 Details of bonding type rmsd covalent geometry : bond 0.00258 (20270) covalent geometry : angle 0.56007 (27439) hydrogen bonds : bond 0.03316 ( 792) hydrogen bonds : angle 4.85945 ( 2196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 504 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 368 MET cc_start: 0.6650 (mmm) cc_final: 0.6246 (mmm) REVERT: U 376 ASP cc_start: 0.6578 (t0) cc_final: 0.6279 (t0) REVERT: U 577 SER cc_start: 0.7654 (m) cc_final: 0.7406 (p) REVERT: U 584 LYS cc_start: 0.7680 (tmmt) cc_final: 0.7151 (tmmt) REVERT: U 588 ARG cc_start: 0.7453 (ttt-90) cc_final: 0.7056 (mtt-85) REVERT: U 644 LYS cc_start: 0.8415 (mttp) cc_final: 0.7995 (mtpt) REVERT: U 754 GLU cc_start: 0.7309 (mp0) cc_final: 0.7055 (mp0) REVERT: U 774 ILE cc_start: 0.7958 (mm) cc_final: 0.7622 (pt) REVERT: U 817 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7377 (mt-10) REVERT: U 897 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8010 (mp) REVERT: U 931 GLU cc_start: 0.7098 (mp0) cc_final: 0.6725 (mp0) REVERT: U 1091 ILE cc_start: 0.7818 (mm) cc_final: 0.7535 (pp) REVERT: U 1105 LEU cc_start: 0.8668 (mp) cc_final: 0.8436 (mp) REVERT: Q 20 SER cc_start: 0.8365 (t) cc_final: 0.8073 (p) REVERT: Q 44 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.8017 (mtm-85) REVERT: Q 101 SER cc_start: 0.8750 (t) cc_final: 0.8481 (p) REVERT: Q 119 ASP cc_start: 0.7840 (t70) cc_final: 0.7609 (t0) REVERT: Q 239 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8034 (ttmm) REVERT: Q 287 LYS cc_start: 0.7196 (tptt) cc_final: 0.6956 (mptt) REVERT: Q 363 TYR cc_start: 0.8306 (m-80) cc_final: 0.7963 (m-80) REVERT: Q 478 SER cc_start: 0.8094 (m) cc_final: 0.7509 (p) REVERT: Q 533 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7671 (mp) REVERT: W 195 LEU cc_start: 0.6769 (tp) cc_final: 0.6039 (mp) REVERT: W 287 ASP cc_start: 0.6773 (t70) cc_final: 0.6473 (t0) REVERT: W 470 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8144 (mt) REVERT: W 489 GLU cc_start: 0.7592 (mp0) cc_final: 0.7341 (pm20) REVERT: W 855 SER cc_start: 0.7832 (m) cc_final: 0.7529 (m) REVERT: W 856 ILE cc_start: 0.8287 (pt) cc_final: 0.8050 (mt) REVERT: W 894 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7224 (tm-30) REVERT: W 905 LYS cc_start: 0.7259 (mmmt) cc_final: 0.6801 (tmtt) REVERT: W 943 ARG cc_start: 0.7906 (mpt180) cc_final: 0.6748 (mmt-90) REVERT: W 1454 LYS cc_start: 0.7850 (ptmm) cc_final: 0.7645 (ptmm) REVERT: W 1463 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7974 (tppt) REVERT: W 1495 PHE cc_start: 0.7329 (m-80) cc_final: 0.7093 (m-80) REVERT: W 1575 MET cc_start: 0.5986 (mtp) cc_final: 0.5614 (mtp) REVERT: S 65 TYR cc_start: 0.8617 (t80) cc_final: 0.8359 (t80) REVERT: S 85 ASN cc_start: 0.7341 (t0) cc_final: 0.7056 (t0) REVERT: S 124 LEU cc_start: 0.8307 (tt) cc_final: 0.8031 (tp) REVERT: S 239 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7923 (m) REVERT: S 301 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8047 (mmmm) REVERT: S 344 SER cc_start: 0.8606 (t) cc_final: 0.8291 (p) REVERT: S 460 MET cc_start: 0.7165 (mmm) cc_final: 0.6943 (mmm) REVERT: S 463 LYS cc_start: 0.7958 (mttt) cc_final: 0.7689 (mttp) REVERT: S 571 GLU cc_start: 0.7348 (mp0) cc_final: 0.6942 (mp0) outliers start: 41 outliers final: 31 residues processed: 519 average time/residue: 0.5840 time to fit residues: 343.8439 Evaluate side-chains 530 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 495 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 572 THR Chi-restraints excluded: chain U residue 645 VAL Chi-restraints excluded: chain U residue 787 ILE Chi-restraints excluded: chain U residue 897 LEU Chi-restraints excluded: chain U residue 1113 VAL Chi-restraints excluded: chain U residue 1141 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 134 SER Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 294 ILE Chi-restraints excluded: chain Q residue 308 LEU Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 512 SER Chi-restraints excluded: chain Q residue 533 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 259 ILE Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 318 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 470 ILE Chi-restraints excluded: chain W residue 542 GLU Chi-restraints excluded: chain W residue 549 LYS Chi-restraints excluded: chain W residue 873 ASP Chi-restraints excluded: chain W residue 986 LEU Chi-restraints excluded: chain W residue 1021 GLN Chi-restraints excluded: chain W residue 1441 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 267 VAL Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 186 optimal weight: 0.0030 chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 191 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 611 GLN U 921 GLN Q 74 GLN ** Q 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 GLN ** Q 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 267 GLN W 435 HIS W 916 ASN W 981 ASN W1059 GLN W1471 ASN ** W1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.153702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135819 restraints weight = 28711.963| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.92 r_work: 0.3725 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20270 Z= 0.148 Angle : 0.576 8.530 27439 Z= 0.296 Chirality : 0.046 0.184 3021 Planarity : 0.004 0.059 3474 Dihedral : 4.390 29.837 2610 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 22.02 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.12 (0.17), residues: 2353 helix: 0.88 (0.19), residues: 788 sheet: -0.21 (0.22), residues: 533 loop : -0.67 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG U 790 TYR 0.026 0.001 TYR W1507 PHE 0.028 0.002 PHE W 328 TRP 0.029 0.001 TRP W1414 HIS 0.007 0.001 HIS W 917 Details of bonding type rmsd covalent geometry : bond 0.00354 (20270) covalent geometry : angle 0.57606 (27439) hydrogen bonds : bond 0.03446 ( 792) hydrogen bonds : angle 4.85149 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9130.49 seconds wall clock time: 156 minutes 2.21 seconds (9362.21 seconds total)