Starting phenix.real_space_refine on Sat Sep 12 23:31:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23fj_68925/09_2026/23fj_68925.cif Found real_map, /net/cci-nas-00/data/ceres_data/23fj_68925/09_2026/23fj_68925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23fj_68925/09_2026/23fj_68925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23fj_68925/09_2026/23fj_68925.map" model { file = "/net/cci-nas-00/data/ceres_data/23fj_68925/09_2026/23fj_68925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23fj_68925/09_2026/23fj_68925.cif" } resolution = 2.96 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= 0.001 sd= 0.019 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 80 5.16 5 C 11772 2.51 5 N 3342 2.21 5 O 3509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18703 Number of models: 1 Model: "" Number of chains: 9 Chain: "K" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1157 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2891 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "O" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 309} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3307 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1419 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Chain: "R" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3718 Classifications: {'peptide': 477} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 441} Chain breaks: 1 Chain: "S" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2885 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 268 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Time building chain proxies: 4.05, per 1000 atoms: 0.22 Number of scatterers: 18703 At special positions: 0 Unit cell: (95.4, 150.52, 198.22, 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 80 16.00 O 3509 8.00 N 3342 7.00 C 11772 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: 1.53 Conformation dependent library (CDL) restraints added in 941.9 milliseconds 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 11 sheets defined 55.6% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'K' and resid 288 through 292 Processing helix chain 'K' and resid 300 through 304 Processing helix chain 'K' and resid 309 through 335 removed outlier: 3.518A pdb=" N GLU K 318 " --> pdb=" O ARG K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 368 removed outlier: 3.525A pdb=" N ALA K 367 " --> pdb=" O MET K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 388 Processing helix chain 'K' and resid 389 through 394 Processing helix chain 'K' and resid 405 through 418 removed outlier: 3.805A pdb=" N ALA K 409 " --> pdb=" O ASN K 405 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU K 413 " --> pdb=" O ALA K 409 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS K 414 " --> pdb=" O ARG K 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 123 No H-bonds generated for 'chain 'N' and resid 121 through 123' Processing helix chain 'N' and resid 131 through 138 removed outlier: 3.534A pdb=" N LEU N 138 " --> pdb=" O GLU N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 168 removed outlier: 3.502A pdb=" N LEU N 167 " --> pdb=" O ASN N 163 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN N 168 " --> pdb=" O ALA N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 180 Processing helix chain 'N' and resid 185 through 199 Processing helix chain 'N' and resid 385 through 399 removed outlier: 3.589A pdb=" N LEU N 390 " --> pdb=" O ASP N 386 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU N 397 " --> pdb=" O LEU N 393 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG N 398 " --> pdb=" O GLU N 394 " (cutoff:3.500A) Processing helix chain 'N' and resid 402 through 411 Processing helix chain 'N' and resid 416 through 423 Processing helix chain 'N' and resid 460 through 470 Processing helix chain 'N' and resid 474 through 482 removed outlier: 4.236A pdb=" N ALA N 480 " --> pdb=" O ALA N 476 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA N 482 " --> pdb=" O THR N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 488 through 496 removed outlier: 3.598A pdb=" N ASN N 492 " --> pdb=" O ILE N 488 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU N 493 " --> pdb=" O LEU N 489 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 633 removed outlier: 3.818A pdb=" N LEU N 551 " --> pdb=" O ALA N 547 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG N 567 " --> pdb=" O SER N 563 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR N 590 " --> pdb=" O LEU N 586 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU N 593 " --> pdb=" O LYS N 589 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET N 594 " --> pdb=" O TYR N 590 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN N 611 " --> pdb=" O ARG N 607 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU N 612 " --> pdb=" O ALA N 608 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG N 631 " --> pdb=" O GLN N 627 " (cutoff:3.500A) Processing helix chain 'N' and resid 645 through 654 removed outlier: 3.657A pdb=" N LEU N 649 " --> pdb=" O ALA N 645 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA N 652 " --> pdb=" O VAL N 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 151 through 167 removed outlier: 3.528A pdb=" N TYR O 155 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 183 removed outlier: 3.771A pdb=" N ASN O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 201 removed outlier: 3.717A pdb=" N GLY O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 400 removed outlier: 3.615A pdb=" N GLU O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 402 through 410 Processing helix chain 'O' and resid 414 through 424 removed outlier: 3.620A pdb=" N VAL O 419 " --> pdb=" O ARG O 415 " (cutoff:3.500A) Processing helix chain 'O' and resid 460 through 472 removed outlier: 3.752A pdb=" N VAL O 465 " --> pdb=" O PRO O 461 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE O 468 " --> pdb=" O SER O 464 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER O 471 " --> pdb=" O SER O 467 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU O 472 " --> pdb=" O PHE O 468 " (cutoff:3.500A) Processing helix chain 'O' and resid 474 through 498 removed outlier: 3.611A pdb=" N ILE O 488 " --> pdb=" O LYS O 484 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 497 " --> pdb=" O LEU O 493 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU O 498 " --> pdb=" O ARG O 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 563 through 634 removed outlier: 3.793A pdb=" N MET O 597 " --> pdb=" O GLU O 593 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG O 621 " --> pdb=" O LEU O 617 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL O 626 " --> pdb=" O ARG O 622 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN O 627 " --> pdb=" O VAL O 623 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU O 630 " --> pdb=" O VAL O 626 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG O 631 " --> pdb=" O GLN O 627 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.515A pdb=" N ASN P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 85 removed outlier: 3.927A pdb=" N ILE P 84 " --> pdb=" O GLY P 80 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL P 85 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 80 through 85' Processing helix chain 'P' and resid 89 through 122 Processing helix chain 'P' and resid 300 through 308 removed outlier: 4.947A pdb=" N ILE P 306 " --> pdb=" O GLU P 302 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 328 removed outlier: 3.737A pdb=" N ASN P 328 " --> pdb=" O TYR P 324 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 348 Processing helix chain 'P' and resid 355 through 360 removed outlier: 3.560A pdb=" N ASN P 360 " --> pdb=" O ILE P 356 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 365 No H-bonds generated for 'chain 'P' and resid 363 through 365' Processing helix chain 'P' and resid 402 through 407 removed outlier: 3.670A pdb=" N THR P 406 " --> pdb=" O ASP P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 415 through 418 Processing helix chain 'P' and resid 419 through 459 removed outlier: 3.528A pdb=" N ASP P 459 " --> pdb=" O GLY P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 479 Processing helix chain 'P' and resid 517 through 523 Processing helix chain 'P' and resid 523 through 528 removed outlier: 3.682A pdb=" N VAL P 527 " --> pdb=" O ALA P 523 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN P 528 " --> pdb=" O ARG P 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 523 through 528' Processing helix chain 'Q' and resid 292 through 297 removed outlier: 3.826A pdb=" N HIS Q 296 " --> pdb=" O ASP Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 316 Processing helix chain 'Q' and resid 323 through 325 No H-bonds generated for 'chain 'Q' and resid 323 through 325' Processing helix chain 'Q' and resid 337 through 341 removed outlier: 3.527A pdb=" N LEU Q 340 " --> pdb=" O LYS Q 337 " (cutoff:3.500A) Processing helix chain 'Q' and resid 352 through 356 Processing helix chain 'Q' and resid 373 through 422 removed outlier: 3.831A pdb=" N ARG Q 377 " --> pdb=" O ALA Q 373 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU Q 382 " --> pdb=" O LYS Q 378 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Q 383 " --> pdb=" O ARG Q 379 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS Q 404 " --> pdb=" O LYS Q 400 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE Q 405 " --> pdb=" O MET Q 401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 452 through 464 removed outlier: 4.008A pdb=" N VAL Q 456 " --> pdb=" O LEU Q 452 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL Q 463 " --> pdb=" O VAL Q 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 753 through 768 removed outlier: 3.952A pdb=" N LYS R 759 " --> pdb=" O ASN R 755 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE R 760 " --> pdb=" O ALA R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 782 through 792 removed outlier: 3.900A pdb=" N GLY R 792 " --> pdb=" O SER R 788 " (cutoff:3.500A) Processing helix chain 'R' and resid 793 through 809 removed outlier: 3.507A pdb=" N VAL R 799 " --> pdb=" O GLY R 795 " (cutoff:3.500A) Processing helix chain 'R' and resid 831 through 852 removed outlier: 4.224A pdb=" N VAL R 835 " --> pdb=" O CYS R 831 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU R 836 " --> pdb=" O GLU R 832 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN R 845 " --> pdb=" O CYS R 841 " (cutoff:3.500A) Processing helix chain 'R' and resid 864 through 875 removed outlier: 3.601A pdb=" N ILE R 874 " --> pdb=" O ARG R 870 " (cutoff:3.500A) Processing helix chain 'R' and resid 876 through 878 No H-bonds generated for 'chain 'R' and resid 876 through 878' Processing helix chain 'R' and resid 887 through 912 removed outlier: 4.377A pdb=" N HIS R 912 " --> pdb=" O ASN R 908 " (cutoff:3.500A) Processing helix chain 'R' and resid 915 through 920 Processing helix chain 'R' and resid 921 through 938 Processing helix chain 'R' and resid 944 through 963 removed outlier: 4.382A pdb=" N THR R 957 " --> pdb=" O LYS R 953 " (cutoff:3.500A) Processing helix chain 'R' and resid 970 through 982 Processing helix chain 'R' and resid 983 through 985 No H-bonds generated for 'chain 'R' and resid 983 through 985' Processing helix chain 'R' and resid 1009 through 1023 removed outlier: 3.865A pdb=" N ARG R1023 " --> pdb=" O LYS R1019 " (cutoff:3.500A) Processing helix chain 'R' and resid 1027 through 1037 Processing helix chain 'R' and resid 1047 through 1059 Processing helix chain 'R' and resid 1074 through 1079 Processing helix chain 'R' and resid 1079 through 1096 Processing helix chain 'R' and resid 1103 through 1110 Processing helix chain 'R' and resid 1114 through 1132 removed outlier: 3.553A pdb=" N THR R1132 " --> pdb=" O ALA R1128 " (cutoff:3.500A) Processing helix chain 'R' and resid 1156 through 1178 removed outlier: 3.774A pdb=" N LEU R1160 " --> pdb=" O ASP R1156 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1202 Processing helix chain 'R' and resid 1207 through 1212 removed outlier: 3.903A pdb=" N LYS R1212 " --> pdb=" O GLU R1209 " (cutoff:3.500A) Processing helix chain 'R' and resid 1214 through 1232 Processing helix chain 'S' and resid 67 through 118 Processing helix chain 'S' and resid 121 through 126 removed outlier: 4.160A pdb=" N LEU S 125 " --> pdb=" O TYR S 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR S 126 " --> pdb=" O PRO S 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 121 through 126' Processing helix chain 'S' and resid 166 through 176 removed outlier: 3.964A pdb=" N MET S 170 " --> pdb=" O SER S 166 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU S 175 " --> pdb=" O LYS S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 220 removed outlier: 3.568A pdb=" N GLU S 218 " --> pdb=" O SER S 214 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET S 220 " --> pdb=" O PHE S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 245 Processing helix chain 'S' and resid 300 through 313 removed outlier: 3.501A pdb=" N ALA S 306 " --> pdb=" O GLU S 302 " (cutoff:3.500A) Processing helix chain 'S' and resid 315 through 340 removed outlier: 3.670A pdb=" N THR S 319 " --> pdb=" O SER S 315 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR S 320 " --> pdb=" O GLY S 316 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA S 323 " --> pdb=" O THR S 319 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE S 333 " --> pdb=" O GLN S 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 353 through 358 removed outlier: 3.814A pdb=" N ALA S 357 " --> pdb=" O ASP S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 369 through 375 removed outlier: 4.202A pdb=" N ASP S 375 " --> pdb=" O GLN S 371 " (cutoff:3.500A) Processing helix chain 'S' and resid 384 through 390 removed outlier: 3.676A pdb=" N ARG S 390 " --> pdb=" O ALA S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 440 through 444 removed outlier: 4.170A pdb=" N ARG S 444 " --> pdb=" O GLU S 441 " (cutoff:3.500A) Processing helix chain 'T' and resid 369 through 396 removed outlier: 3.688A pdb=" N MET T 386 " --> pdb=" O GLN T 382 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG T 387 " --> pdb=" O GLN T 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'U' and resid 75 through 84 removed outlier: 3.506A pdb=" N LEU U 79 " --> pdb=" O SER U 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 286 through 287 removed outlier: 6.746A pdb=" N ILE K 286 " --> pdb=" O GLU Q 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'N' and resid 116 through 119 Processing sheet with id=AA3, first strand: chain 'N' and resid 661 through 662 removed outlier: 3.933A pdb=" N THR Q 468 " --> pdb=" O THR N 662 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 162 through 170 removed outlier: 3.676A pdb=" N GLU P 139 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG P 164 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 137 " --> pdb=" O ARG P 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER P 135 " --> pdb=" O LYS P 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG P 131 " --> pdb=" O ARG P 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 227 through 228 removed outlier: 4.239A pdb=" N LEU P 288 " --> pdb=" O ILE P 373 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE P 373 " --> pdb=" O LEU P 288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 311 through 312 removed outlier: 3.815A pdb=" N GLU P 298 " --> pdb=" O ARG P 368 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG P 368 " --> pdb=" O GLU P 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 779 through 781 removed outlier: 6.211A pdb=" N VAL R 780 " --> pdb=" O ILE S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 812 through 816 removed outlier: 3.513A pdb=" N PHE R 821 " --> pdb=" O HIS R 813 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL R 815 " --> pdb=" O HIS R 819 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS R 819 " --> pdb=" O VAL R 815 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 991 through 992 Processing sheet with id=AB1, first strand: chain 'S' and resid 180 through 186 Processing sheet with id=AB2, first strand: chain 'S' and resid 379 through 382 removed outlier: 3.764A pdb=" N HIS S 284 " --> pdb=" O ILE S 281 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR S 423 " --> pdb=" O LYS S 276 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN S 278 " --> pdb=" O THR S 423 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2673 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: 3.20 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3211 1.31 - 1.44: 4837 1.44 - 1.57: 10891 1.57 - 1.69: 0 1.69 - 1.82: 140 Bond restraints: 19079 Sorted by residual: bond pdb=" CA ALA N 482 " pdb=" CB ALA N 482 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.46e-02 4.69e+03 2.96e+01 bond pdb=" C MET N 161 " pdb=" O MET N 161 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.15e-02 7.56e+03 2.01e+01 bond pdb=" CA ALA N 480 " pdb=" CB ALA N 480 " ideal model delta sigma weight residual 1.534 1.477 0.056 1.58e-02 4.01e+03 1.26e+01 bond pdb=" CA ALA N 479 " pdb=" CB ALA N 479 " ideal model delta sigma weight residual 1.532 1.469 0.064 1.79e-02 3.12e+03 1.26e+01 bond pdb=" C ARG S 107 " pdb=" O ARG S 107 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.15e-02 7.56e+03 1.21e+01 ... (remaining 19074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 25019 2.03 - 4.06: 682 4.06 - 6.10: 72 6.10 - 8.13: 21 8.13 - 10.16: 5 Bond angle restraints: 25799 Sorted by residual: angle pdb=" N TYR O 205 " pdb=" CA TYR O 205 " pdb=" C TYR O 205 " ideal model delta sigma weight residual 113.55 103.53 10.02 1.26e+00 6.30e-01 6.32e+01 angle pdb=" N ARG R1069 " pdb=" CA ARG R1069 " pdb=" C ARG R1069 " ideal model delta sigma weight residual 110.65 101.96 8.69 1.26e+00 6.30e-01 4.75e+01 angle pdb=" N ALA N 482 " pdb=" CA ALA N 482 " pdb=" C ALA N 482 " ideal model delta sigma weight residual 112.72 106.19 6.53 1.14e+00 7.69e-01 3.28e+01 angle pdb=" C ALA N 668 " pdb=" CA ALA N 668 " pdb=" CB ALA N 668 " ideal model delta sigma weight residual 116.54 109.96 6.58 1.15e+00 7.56e-01 3.28e+01 angle pdb=" N ASN N 144 " pdb=" CA ASN N 144 " pdb=" C ASN N 144 " ideal model delta sigma weight residual 112.86 106.42 6.44 1.22e+00 6.72e-01 2.78e+01 ... (remaining 25794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 10168 17.81 - 35.62: 1197 35.62 - 53.43: 288 53.43 - 71.24: 62 71.24 - 89.05: 19 Dihedral angle restraints: 11734 sinusoidal: 4891 harmonic: 6843 Sorted by residual: dihedral pdb=" C HIS R1070 " pdb=" N HIS R1070 " pdb=" CA HIS R1070 " pdb=" CB HIS R1070 " ideal model delta harmonic sigma weight residual -122.60 -133.37 10.77 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" CA PRO R 986 " pdb=" C PRO R 986 " pdb=" N GLN R 987 " pdb=" CA GLN R 987 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASN S 140 " pdb=" C ASN S 140 " pdb=" N GLY S 141 " pdb=" CA GLY S 141 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 11731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2418 0.060 - 0.120: 342 0.120 - 0.180: 54 0.180 - 0.239: 10 0.239 - 0.299: 1 Chirality restraints: 2825 Sorted by residual: chirality pdb=" CA HIS R1070 " pdb=" N HIS R1070 " pdb=" C HIS R1070 " pdb=" CB HIS R1070 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LEU O 183 " pdb=" N LEU O 183 " pdb=" C LEU O 183 " pdb=" CB LEU O 183 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR O 205 " pdb=" N TYR O 205 " pdb=" C TYR O 205 " pdb=" CB TYR O 205 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2822 not shown) Planarity restraints: 3403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN S 296 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO S 297 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO S 297 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO S 297 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 751 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLY R 751 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY R 751 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS R 752 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR N 478 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C THR N 478 " -0.056 2.00e-02 2.50e+03 pdb=" O THR N 478 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA N 479 " 0.019 2.00e-02 2.50e+03 ... (remaining 3400 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1243 2.74 - 3.28: 19957 3.28 - 3.82: 30968 3.82 - 4.36: 38292 4.36 - 4.90: 62461 Nonbonded interactions: 152921 Sorted by model distance: nonbonded pdb=" OG1 THR K 393 " pdb=" OD2 ASP P 488 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR K 386 " pdb=" OE1 GLN O 235 " model vdw 2.208 3.040 nonbonded pdb=" NZ LYS N 583 " pdb=" OD1 ASP P 433 " model vdw 2.228 3.120 nonbonded pdb=" OE2 GLU Q 312 " pdb=" OH TYR R 749 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR S 160 " pdb=" OE2 GLU S 218 " model vdw 2.246 3.040 ... (remaining 152916 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: 10.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.079 19079 Z= 0.278 Angle : 0.729 10.160 25799 Z= 0.455 Chirality : 0.045 0.299 2825 Planarity : 0.005 0.104 3403 Dihedral : 16.356 89.049 7276 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.02 % Favored : 92.94 % Rotamer: Outliers : 0.40 % Allowed : 21.49 % Favored : 78.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.17), residues: 2293 helix: 0.04 (0.15), residues: 1198 sheet: -1.13 (0.58), residues: 81 loop : -1.95 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 484 TYR 0.043 0.001 TYR K 369 PHE 0.022 0.001 PHE O 196 TRP 0.048 0.002 TRP S 189 HIS 0.008 0.001 HIS R1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.28 (19079) covalent geometry : angle 0.72946 / 0.46 (25799) hydrogen bonds : bond 0.24898 / 16.79 ( 912) hydrogen bonds : angle 7.46660 / 5.36 ( 2673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 703 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 311 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7639 (mm-30) REVERT: K 320 ILE cc_start: 0.9180 (mp) cc_final: 0.8955 (mp) REVERT: N 226 ILE cc_start: 0.8892 (tp) cc_final: 0.8646 (tt) REVERT: N 393 LEU cc_start: 0.7799 (mt) cc_final: 0.7167 (mm) REVERT: N 424 GLN cc_start: 0.7836 (mt0) cc_final: 0.7091 (mt0) REVERT: N 489 LEU cc_start: 0.8886 (mt) cc_final: 0.8642 (tp) REVERT: N 595 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6862 (tm-30) REVERT: N 599 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8141 (mm110) REVERT: N 607 ARG cc_start: 0.8375 (ptp-170) cc_final: 0.8095 (ptm-80) REVERT: N 624 ARG cc_start: 0.8109 (mmp80) cc_final: 0.7672 (mmp80) REVERT: O 182 ASN cc_start: 0.7676 (m-40) cc_final: 0.7461 (m110) REVERT: O 394 GLU cc_start: 0.7031 (tt0) cc_final: 0.6311 (tt0) REVERT: O 405 GLN cc_start: 0.7945 (mp10) cc_final: 0.7422 (mt0) REVERT: O 430 LYS cc_start: 0.8589 (tttt) cc_final: 0.8278 (tttt) REVERT: O 492 ASN cc_start: 0.7683 (t0) cc_final: 0.7461 (t0) REVERT: O 568 GLU cc_start: 0.7856 (tp30) cc_final: 0.7552 (tp30) REVERT: O 590 TYR cc_start: 0.8376 (m-10) cc_final: 0.7941 (m-10) REVERT: O 599 GLN cc_start: 0.8088 (mm110) cc_final: 0.7714 (mm110) REVERT: P 64 LEU cc_start: 0.8641 (mp) cc_final: 0.8397 (mm) REVERT: P 115 ASP cc_start: 0.7842 (m-30) cc_final: 0.7398 (m-30) REVERT: P 126 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7046 (tmt90) REVERT: P 128 LYS cc_start: 0.7843 (tptm) cc_final: 0.7248 (tptp) REVERT: P 290 ARG cc_start: 0.6609 (ptm160) cc_final: 0.6202 (pmm-80) REVERT: P 293 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.5635 (t70) REVERT: P 297 PHE cc_start: 0.7289 (m-80) cc_final: 0.6748 (m-80) REVERT: P 315 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7842 (tp-100) REVERT: P 516 SER cc_start: 0.7692 (t) cc_final: 0.7488 (t) REVERT: Q 293 MET cc_start: 0.7373 (ptt) cc_final: 0.7152 (ptt) REVERT: Q 301 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7172 (mp0) REVERT: Q 380 VAL cc_start: 0.8934 (p) cc_final: 0.8670 (t) REVERT: Q 390 GLU cc_start: 0.8424 (tt0) cc_final: 0.8142 (tt0) REVERT: Q 411 ILE cc_start: 0.7690 (tt) cc_final: 0.7231 (tt) REVERT: Q 458 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7607 (ttp-110) REVERT: Q 460 GLU cc_start: 0.8248 (tt0) cc_final: 0.8011 (tt0) REVERT: R 765 GLN cc_start: 0.7734 (pp30) cc_final: 0.7443 (pp30) REVERT: R 818 ASN cc_start: 0.8250 (p0) cc_final: 0.7625 (t0) REVERT: R 922 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7070 (tm-30) REVERT: R 926 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7886 (mttt) REVERT: R 946 ASN cc_start: 0.8801 (t0) cc_final: 0.8519 (t0) REVERT: R 987 GLN cc_start: 0.7456 (tp40) cc_final: 0.7094 (tp40) REVERT: R 991 THR cc_start: 0.8877 (p) cc_final: 0.8659 (p) REVERT: R 1160 LEU cc_start: 0.8806 (tt) cc_final: 0.8550 (tm) REVERT: R 1171 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7722 (ttp80) REVERT: S 91 LYS cc_start: 0.8763 (tppt) cc_final: 0.8479 (tppt) REVERT: S 140 ASN cc_start: 0.8091 (m-40) cc_final: 0.7796 (m-40) REVERT: S 163 LEU cc_start: 0.8442 (tp) cc_final: 0.8219 (tm) REVERT: S 178 GLU cc_start: 0.8609 (pt0) cc_final: 0.8379 (pt0) REVERT: S 215 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7532 (tp-100) REVERT: S 269 ASP cc_start: 0.7961 (t70) cc_final: 0.7598 (t0) REVERT: S 289 GLN cc_start: 0.7229 (pt0) cc_final: 0.6701 (pt0) REVERT: S 295 ASN cc_start: 0.8606 (p0) cc_final: 0.7998 (p0) REVERT: S 302 GLU cc_start: 0.8396 (mp0) cc_final: 0.7913 (pm20) REVERT: S 375 ASP cc_start: 0.8081 (t0) cc_final: 0.7629 (t0) REVERT: S 382 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6441 (tm-30) REVERT: T 365 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8089 (tm-30) REVERT: T 386 MET cc_start: 0.8252 (mtm) cc_final: 0.7962 (mpp) outliers start: 8 outliers final: 5 residues processed: 707 average time/residue: 0.7496 time to fit residues: 584.4178 Evaluate side-chains 574 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 568 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 293 ASP Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 ASN N 405 GLN N 599 GLN N 627 GLN O 199 GLN P 315 GLN P 328 ASN P 471 GLN P 522 ASN Q 309 GLN Q 357 GLN Q 398 HIS R 830 HIS R 881 ASN R 893 ASN R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1068 HIS ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1125 GLN S 94 GLN S 120 ASN ** S 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 329 GLN T 383 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.140975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120545 restraints weight = 37217.421| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.03 r_work: 0.3625 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19079 Z= 0.174 Angle : 0.700 10.062 25799 Z= 0.361 Chirality : 0.043 0.234 2825 Planarity : 0.005 0.063 3403 Dihedral : 4.719 38.578 2579 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.90 % Allowed : 25.89 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.18), residues: 2293 helix: 0.87 (0.14), residues: 1225 sheet: -1.43 (0.54), residues: 82 loop : -1.87 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 602 TYR 0.021 0.002 TYR O 166 PHE 0.037 0.002 PHE O 196 TRP 0.029 0.002 TRP S 189 HIS 0.007 0.001 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (19079) covalent geometry : angle 0.70043 / 0.36 (25799) hydrogen bonds : bond 0.05587 / 3.73 ( 912) hydrogen bonds : angle 4.69616 / 3.34 ( 2673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 607 time to evaluate : 0.804 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: K 311 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7855 (mm-30) REVERT: K 320 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8801 (mp) REVERT: K 407 ARG cc_start: 0.8201 (tmm160) cc_final: 0.7818 (tmm-80) REVERT: N 140 GLU cc_start: 0.8366 (tt0) cc_final: 0.8043 (tp30) REVERT: N 159 ASP cc_start: 0.8280 (m-30) cc_final: 0.7749 (m-30) REVERT: N 206 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8461 (m) REVERT: N 224 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8297 (mtpt) REVERT: N 227 VAL cc_start: 0.8705 (p) cc_final: 0.8375 (m) REVERT: N 424 GLN cc_start: 0.8120 (mt0) cc_final: 0.7709 (mt0) REVERT: N 427 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7790 (pp) REVERT: N 580 MET cc_start: 0.8615 (mmm) cc_final: 0.8344 (mmm) REVERT: N 595 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7716 (tm-30) REVERT: N 599 GLN cc_start: 0.8860 (mm110) cc_final: 0.8640 (mm-40) REVERT: N 607 ARG cc_start: 0.8666 (ptp-170) cc_final: 0.8450 (ptm-80) REVERT: O 127 ASP cc_start: 0.6089 (p0) cc_final: 0.5874 (p0) REVERT: O 128 MET cc_start: 0.8563 (tmt) cc_final: 0.7728 (tmm) REVERT: O 133 ASP cc_start: 0.7588 (m-30) cc_final: 0.7364 (t0) REVERT: O 386 ASP cc_start: 0.7773 (p0) cc_final: 0.7541 (p0) REVERT: O 402 ASP cc_start: 0.7403 (t0) cc_final: 0.7034 (t0) REVERT: O 405 GLN cc_start: 0.8027 (mp10) cc_final: 0.7736 (mt0) REVERT: O 409 TYR cc_start: 0.8621 (t80) cc_final: 0.8263 (t80) REVERT: O 430 LYS cc_start: 0.8835 (tttt) cc_final: 0.8447 (tttt) REVERT: O 490 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8252 (mttm) REVERT: O 568 GLU cc_start: 0.8045 (tp30) cc_final: 0.7271 (tp30) REVERT: O 569 MET cc_start: 0.8347 (mpp) cc_final: 0.7975 (mpp) REVERT: O 595 GLU cc_start: 0.7299 (tp30) cc_final: 0.7094 (mm-30) REVERT: O 599 GLN cc_start: 0.8511 (mm110) cc_final: 0.8161 (mm110) REVERT: O 603 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7796 (mpp-170) REVERT: O 607 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7307 (tpp80) REVERT: P 119 SER cc_start: 0.8058 (t) cc_final: 0.7787 (p) REVERT: P 250 TRP cc_start: 0.5499 (OUTLIER) cc_final: 0.5283 (t-100) REVERT: P 288 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6641 (tm) REVERT: P 290 ARG cc_start: 0.6890 (ptm160) cc_final: 0.6572 (pmm-80) REVERT: P 297 PHE cc_start: 0.7646 (m-80) cc_final: 0.7189 (m-80) REVERT: P 319 MET cc_start: 0.8118 (tmm) cc_final: 0.7855 (tmm) REVERT: P 427 LYS cc_start: 0.8589 (mttt) cc_final: 0.8199 (mptt) REVERT: P 516 SER cc_start: 0.8265 (t) cc_final: 0.8016 (t) REVERT: Q 286 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7158 (mm-30) REVERT: Q 293 MET cc_start: 0.7912 (ptt) cc_final: 0.7660 (ptt) REVERT: Q 300 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7160 (ttp80) REVERT: Q 312 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: Q 315 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7851 (tm-30) REVERT: R 762 GLU cc_start: 0.8215 (tp30) cc_final: 0.7871 (tp30) REVERT: R 843 GLU cc_start: 0.8418 (tp30) cc_final: 0.7933 (tm-30) REVERT: R 845 GLN cc_start: 0.8306 (mp10) cc_final: 0.7852 (mp10) REVERT: R 847 ASP cc_start: 0.8304 (m-30) cc_final: 0.8053 (OUTLIER) REVERT: R 922 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7557 (tm-30) REVERT: R 926 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8162 (mttt) REVERT: R 946 ASN cc_start: 0.8607 (t0) cc_final: 0.8265 (t0) REVERT: R 987 GLN cc_start: 0.7875 (tp40) cc_final: 0.7568 (tp40) REVERT: R 1117 GLN cc_start: 0.8246 (mt0) cc_final: 0.8024 (mt0) REVERT: R 1158 ASP cc_start: 0.8599 (m-30) cc_final: 0.8321 (m-30) REVERT: R 1160 LEU cc_start: 0.8991 (tt) cc_final: 0.8706 (tm) REVERT: R 1191 ASN cc_start: 0.8622 (p0) cc_final: 0.8025 (p0) REVERT: S 91 LYS cc_start: 0.8746 (tppt) cc_final: 0.8363 (tppt) REVERT: S 140 ASN cc_start: 0.8038 (m-40) cc_final: 0.7695 (m-40) REVERT: S 201 ASN cc_start: 0.8303 (t0) cc_final: 0.8095 (t0) REVERT: S 241 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7963 (mt-10) REVERT: S 285 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8341 (t) REVERT: S 293 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6550 (m-30) REVERT: S 295 ASN cc_start: 0.8573 (p0) cc_final: 0.7949 (p0) REVERT: S 303 GLU cc_start: 0.8348 (tp30) cc_final: 0.7750 (tp30) REVERT: S 313 SER cc_start: 0.8995 (t) cc_final: 0.8630 (p) REVERT: S 334 THR cc_start: 0.8478 (m) cc_final: 0.8101 (p) REVERT: S 354 LEU cc_start: 0.8162 (mp) cc_final: 0.7937 (mp) REVERT: S 375 ASP cc_start: 0.8238 (t0) cc_final: 0.7639 (t0) REVERT: S 442 GLU cc_start: 0.8000 (mp0) cc_final: 0.7671 (mp0) REVERT: T 361 THR cc_start: 0.6559 (m) cc_final: 0.5983 (m) REVERT: T 365 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8186 (tm-30) REVERT: U 83 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7942 (mpt-90) outliers start: 78 outliers final: 30 residues processed: 645 average time/residue: 0.7321 time to fit residues: 522.3168 Evaluate side-chains 616 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 578 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain N residue 659 ASN Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 598 LEU Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 250 TRP Chi-restraints excluded: chain P residue 285 ILE Chi-restraints excluded: chain P residue 288 LEU Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain R residue 745 LYS Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 856 THR Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 274 LEU Chi-restraints excluded: chain S residue 285 THR Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 293 ASP Chi-restraints excluded: chain S residue 430 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 164 optimal weight: 1.9990 chunk 199 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 84 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 142 optimal weight: 0.0970 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 130 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 388 ASN K 404 HIS N 143 ASN N 203 ASN O 169 ASN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 424 GLN P 522 ASN R 830 HIS R 881 ASN R 915 ASN R 961 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN ** S 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.121123 restraints weight = 37534.075| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.06 r_work: 0.3639 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19079 Z= 0.144 Angle : 0.661 11.204 25799 Z= 0.336 Chirality : 0.041 0.203 2825 Planarity : 0.005 0.068 3403 Dihedral : 4.567 36.931 2571 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.55 % Allowed : 27.19 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2293 helix: 1.15 (0.15), residues: 1233 sheet: -1.53 (0.55), residues: 82 loop : -1.90 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 458 TYR 0.029 0.002 TYR K 369 PHE 0.037 0.001 PHE O 196 TRP 0.028 0.001 TRP S 189 HIS 0.005 0.001 HIS P 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (19079) covalent geometry : angle 0.66085 / 0.34 (25799) hydrogen bonds : bond 0.04802 / 3.19 ( 912) hydrogen bonds : angle 4.44091 / 3.14 ( 2673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 588 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 311 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7851 (mm-30) REVERT: K 320 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8711 (mp) REVERT: K 335 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7025 (tm) REVERT: K 358 LYS cc_start: 0.7589 (mmmt) cc_final: 0.7329 (mmmm) REVERT: K 407 ARG cc_start: 0.8204 (tmm160) cc_final: 0.7820 (tmm-80) REVERT: N 159 ASP cc_start: 0.8275 (m-30) cc_final: 0.7791 (m-30) REVERT: N 180 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.8086 (ttm-80) REVERT: N 190 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7127 (ttt) REVERT: N 206 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8472 (m) REVERT: N 224 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8203 (mtpt) REVERT: N 424 GLN cc_start: 0.8179 (mt0) cc_final: 0.7950 (mt0) REVERT: N 595 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7738 (tm-30) REVERT: N 607 ARG cc_start: 0.8661 (ptp-170) cc_final: 0.8426 (ptm-80) REVERT: N 624 ARG cc_start: 0.7692 (mmp80) cc_final: 0.7431 (mmp80) REVERT: N 659 ASN cc_start: 0.1709 (OUTLIER) cc_final: 0.1316 (p0) REVERT: O 156 LYS cc_start: 0.8393 (ptmm) cc_final: 0.7766 (pttt) REVERT: O 192 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8519 (mpp80) REVERT: O 386 ASP cc_start: 0.7817 (p0) cc_final: 0.7537 (p0) REVERT: O 402 ASP cc_start: 0.7369 (t0) cc_final: 0.6911 (t0) REVERT: O 405 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: O 409 TYR cc_start: 0.8644 (t80) cc_final: 0.8362 (t80) REVERT: O 430 LYS cc_start: 0.8855 (tttt) cc_final: 0.8472 (tttt) REVERT: O 474 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7772 (p0) REVERT: O 490 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8173 (mttm) REVERT: O 571 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8033 (ttp80) REVERT: O 599 GLN cc_start: 0.8402 (mm110) cc_final: 0.8001 (mm-40) REVERT: O 603 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7799 (mpp-170) REVERT: O 607 ARG cc_start: 0.7735 (tpp80) cc_final: 0.7250 (tpp80) REVERT: P 102 GLU cc_start: 0.8007 (tt0) cc_final: 0.7652 (tm-30) REVERT: P 130 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.3633 (ttm) REVERT: P 220 PHE cc_start: 0.6098 (t80) cc_final: 0.5324 (t80) REVERT: P 297 PHE cc_start: 0.7659 (m-80) cc_final: 0.7359 (m-80) REVERT: P 319 MET cc_start: 0.8099 (tmm) cc_final: 0.7816 (tmm) REVERT: P 426 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8260 (mm) REVERT: P 487 ARG cc_start: 0.9127 (mmm-85) cc_final: 0.8867 (mmm-85) REVERT: P 514 LYS cc_start: 0.6737 (ttmt) cc_final: 0.6302 (ttpt) REVERT: P 516 SER cc_start: 0.8259 (t) cc_final: 0.8027 (t) REVERT: P 524 ARG cc_start: 0.7428 (tpp80) cc_final: 0.7077 (tpp80) REVERT: Q 285 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7801 (tp30) REVERT: Q 300 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7290 (ttm170) REVERT: Q 312 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: Q 315 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7786 (tm-30) REVERT: Q 395 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8312 (tmmt) REVERT: R 843 GLU cc_start: 0.8441 (tp30) cc_final: 0.7946 (tm-30) REVERT: R 845 GLN cc_start: 0.8239 (mp10) cc_final: 0.7830 (mp10) REVERT: R 847 ASP cc_start: 0.8324 (m-30) cc_final: 0.8069 (t0) REVERT: R 922 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7728 (tm-30) REVERT: R 946 ASN cc_start: 0.8550 (t0) cc_final: 0.8205 (t0) REVERT: R 1115 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8537 (p90) REVERT: R 1117 GLN cc_start: 0.8271 (mt0) cc_final: 0.8031 (mt0) REVERT: R 1158 ASP cc_start: 0.8591 (m-30) cc_final: 0.8304 (m-30) REVERT: R 1160 LEU cc_start: 0.8901 (tt) cc_final: 0.8620 (tm) REVERT: R 1171 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8165 (tmm-80) REVERT: R 1191 ASN cc_start: 0.8661 (p0) cc_final: 0.8020 (p0) REVERT: R 1218 ASP cc_start: 0.7800 (m-30) cc_final: 0.7599 (t70) REVERT: R 1230 VAL cc_start: 0.5397 (OUTLIER) cc_final: 0.4483 (t) REVERT: S 91 LYS cc_start: 0.8670 (tppt) cc_final: 0.8327 (tppt) REVERT: S 140 ASN cc_start: 0.8057 (m-40) cc_final: 0.7734 (m-40) REVERT: S 163 LEU cc_start: 0.8703 (tp) cc_final: 0.8493 (mp) REVERT: S 201 ASN cc_start: 0.8270 (t0) cc_final: 0.8000 (t0) REVERT: S 231 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8083 (p) REVERT: S 285 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8355 (t) REVERT: S 303 GLU cc_start: 0.8332 (tp30) cc_final: 0.7811 (tp30) REVERT: S 313 SER cc_start: 0.8971 (t) cc_final: 0.8521 (p) REVERT: S 334 THR cc_start: 0.8437 (m) cc_final: 0.8058 (p) REVERT: S 354 LEU cc_start: 0.8054 (mp) cc_final: 0.7812 (mp) REVERT: S 375 ASP cc_start: 0.8179 (t0) cc_final: 0.7570 (t0) REVERT: S 442 GLU cc_start: 0.7956 (mp0) cc_final: 0.7588 (mp0) REVERT: T 361 THR cc_start: 0.6657 (m) cc_final: 0.6117 (m) REVERT: T 365 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8196 (tm-30) REVERT: T 386 MET cc_start: 0.8325 (mpp) cc_final: 0.8092 (pmm) REVERT: T 387 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7843 (ptp90) REVERT: T 392 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: U 71 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6401 (mm) REVERT: U 76 GLN cc_start: 0.8297 (mt0) cc_final: 0.7994 (mm-40) REVERT: U 83 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7962 (mpt-90) outliers start: 91 outliers final: 29 residues processed: 639 average time/residue: 0.7069 time to fit residues: 500.2728 Evaluate side-chains 613 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 566 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 190 MET Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain N residue 659 ASN Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 192 ARG Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 130 MET Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 285 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 765 GLN Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1230 VAL Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 169 ASP Chi-restraints excluded: chain S residue 231 VAL Chi-restraints excluded: chain S residue 274 LEU Chi-restraints excluded: chain S residue 285 THR Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 392 ASN Chi-restraints excluded: chain U residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 73 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 143 ASN N 203 ASN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 338 ASN R 830 HIS R 881 ASN R 912 HIS R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN ** S 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.137101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.117269 restraints weight = 37437.035| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.04 r_work: 0.3584 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19079 Z= 0.247 Angle : 0.722 9.131 25799 Z= 0.369 Chirality : 0.045 0.197 2825 Planarity : 0.005 0.065 3403 Dihedral : 4.782 40.725 2571 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 5.35 % Allowed : 27.99 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.18), residues: 2293 helix: 1.10 (0.14), residues: 1221 sheet: -1.78 (0.49), residues: 94 loop : -1.89 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 112 TYR 0.030 0.002 TYR P 362 PHE 0.039 0.002 PHE O 196 TRP 0.033 0.003 TRP S 189 HIS 0.007 0.001 HIS P 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (19079) covalent geometry : angle 0.72210 / 0.37 (25799) hydrogen bonds : bond 0.04827 / 3.22 ( 912) hydrogen bonds : angle 4.48009 / 3.16 ( 2673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 589 time to evaluate : 0.746 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: K 311 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7850 (mm-30) REVERT: K 320 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8717 (mp) REVERT: K 358 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7383 (mmmm) REVERT: K 362 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8619 (mt-10) REVERT: K 363 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7838 (ttm) REVERT: K 407 ARG cc_start: 0.8244 (tmm160) cc_final: 0.7856 (tmm-80) REVERT: K 413 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: N 180 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8257 (ttm-80) REVERT: N 209 ASP cc_start: 0.8519 (t0) cc_final: 0.8294 (t0) REVERT: N 224 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8155 (mtpp) REVERT: N 423 LEU cc_start: 0.7977 (tt) cc_final: 0.7748 (tt) REVERT: N 424 GLN cc_start: 0.8250 (mt0) cc_final: 0.7885 (mt0) REVERT: N 595 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7786 (tm-30) REVERT: O 128 MET cc_start: 0.8710 (tmt) cc_final: 0.8080 (tmm) REVERT: O 133 ASP cc_start: 0.7533 (m-30) cc_final: 0.7257 (t0) REVERT: O 156 LYS cc_start: 0.8466 (ptmm) cc_final: 0.7848 (pttt) REVERT: O 386 ASP cc_start: 0.7908 (p0) cc_final: 0.7647 (p0) REVERT: O 394 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8157 (mp0) REVERT: O 402 ASP cc_start: 0.7443 (t0) cc_final: 0.6973 (t0) REVERT: O 405 GLN cc_start: 0.8142 (mp10) cc_final: 0.7832 (mt0) REVERT: O 409 TYR cc_start: 0.8868 (t80) cc_final: 0.8257 (t80) REVERT: O 430 LYS cc_start: 0.8858 (tttt) cc_final: 0.8459 (tttt) REVERT: O 474 ASP cc_start: 0.8311 (t70) cc_final: 0.7621 (p0) REVERT: O 490 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8267 (mtmm) REVERT: O 571 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8147 (ttp80) REVERT: O 607 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7275 (tpp80) REVERT: O 610 GLN cc_start: 0.8094 (pp30) cc_final: 0.7883 (pp30) REVERT: P 64 LEU cc_start: 0.8704 (mm) cc_final: 0.8353 (tp) REVERT: P 71 LYS cc_start: 0.8931 (tppp) cc_final: 0.8660 (tppp) REVERT: P 127 TYR cc_start: 0.6196 (t80) cc_final: 0.5221 (t80) REVERT: P 220 PHE cc_start: 0.5844 (t80) cc_final: 0.5031 (m-80) REVERT: P 297 PHE cc_start: 0.7718 (m-80) cc_final: 0.7441 (m-80) REVERT: P 319 MET cc_start: 0.8106 (tmm) cc_final: 0.7763 (tmm) REVERT: P 514 LYS cc_start: 0.6794 (ttmt) cc_final: 0.6156 (ttpt) REVERT: P 524 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7225 (tpp80) REVERT: Q 286 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7235 (mt-10) REVERT: Q 312 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: Q 315 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7789 (tm-30) REVERT: Q 378 LYS cc_start: 0.8737 (tmmm) cc_final: 0.8536 (ttpp) REVERT: Q 395 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8312 (tmmt) REVERT: R 843 GLU cc_start: 0.8428 (tp30) cc_final: 0.7925 (tm-30) REVERT: R 845 GLN cc_start: 0.8295 (mp10) cc_final: 0.7885 (mp10) REVERT: R 847 ASP cc_start: 0.8339 (m-30) cc_final: 0.8044 (t0) REVERT: R 922 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7528 (tm-30) REVERT: R 926 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8214 (mttt) REVERT: R 946 ASN cc_start: 0.8585 (t0) cc_final: 0.8259 (t0) REVERT: R 1115 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8568 (p90) REVERT: R 1117 GLN cc_start: 0.8367 (mt0) cc_final: 0.8143 (mt0) REVERT: R 1158 ASP cc_start: 0.8625 (m-30) cc_final: 0.8328 (m-30) REVERT: R 1160 LEU cc_start: 0.8893 (tt) cc_final: 0.8641 (tm) REVERT: R 1191 ASN cc_start: 0.8733 (p0) cc_final: 0.8171 (p0) REVERT: R 1218 ASP cc_start: 0.7871 (m-30) cc_final: 0.7629 (t0) REVERT: R 1230 VAL cc_start: 0.5478 (OUTLIER) cc_final: 0.4650 (t) REVERT: S 66 ARG cc_start: 0.6389 (pmm150) cc_final: 0.5948 (pmm150) REVERT: S 74 MET cc_start: 0.8410 (tmm) cc_final: 0.7994 (tmm) REVERT: S 140 ASN cc_start: 0.8137 (m-40) cc_final: 0.7823 (m-40) REVERT: S 193 LYS cc_start: 0.8096 (tttp) cc_final: 0.7887 (ttmp) REVERT: S 201 ASN cc_start: 0.8451 (t0) cc_final: 0.8179 (t0) REVERT: S 272 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6741 (ttp80) REVERT: S 303 GLU cc_start: 0.8443 (tp30) cc_final: 0.7920 (tp30) REVERT: S 313 SER cc_start: 0.8991 (t) cc_final: 0.8566 (p) REVERT: S 334 THR cc_start: 0.8423 (m) cc_final: 0.8038 (p) REVERT: S 354 LEU cc_start: 0.8019 (mp) cc_final: 0.7783 (mp) REVERT: S 375 ASP cc_start: 0.8293 (t0) cc_final: 0.7718 (t0) REVERT: S 428 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8139 (pp) REVERT: S 442 GLU cc_start: 0.8033 (mp0) cc_final: 0.7603 (mp0) REVERT: T 361 THR cc_start: 0.6275 (m) cc_final: 0.5725 (m) REVERT: T 365 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8207 (tm-30) REVERT: T 392 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7952 (m-40) REVERT: U 76 GLN cc_start: 0.8353 (mt0) cc_final: 0.8061 (mm-40) REVERT: U 83 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7918 (mpt-90) outliers start: 107 outliers final: 42 residues processed: 649 average time/residue: 0.7026 time to fit residues: 505.3361 Evaluate side-chains 629 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 579 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 192 ARG Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 285 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 285 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 765 GLN Chi-restraints excluded: chain R residue 775 LEU Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 856 THR Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 930 VAL Chi-restraints excluded: chain R residue 997 LEU Chi-restraints excluded: chain R residue 1007 HIS Chi-restraints excluded: chain R residue 1093 MET Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain R residue 1230 VAL Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 392 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 99 optimal weight: 0.0050 chunk 208 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 14 optimal weight: 0.0980 chunk 180 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 overall best weight: 0.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 404 HIS N 112 GLN N 203 ASN O 169 ASN O 182 ASN O 491 GLN P 522 ASN R 830 HIS R 881 ASN R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN S 173 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121225 restraints weight = 37085.680| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.05 r_work: 0.3634 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19079 Z= 0.136 Angle : 0.685 10.011 25799 Z= 0.345 Chirality : 0.041 0.203 2825 Planarity : 0.005 0.078 3403 Dihedral : 4.636 37.917 2571 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.55 % Allowed : 29.84 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.18), residues: 2293 helix: 1.29 (0.15), residues: 1235 sheet: -1.97 (0.48), residues: 107 loop : -1.95 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 112 TYR 0.039 0.002 TYR K 369 PHE 0.040 0.002 PHE O 196 TRP 0.039 0.002 TRP S 189 HIS 0.008 0.001 HIS P 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (19079) covalent geometry : angle 0.68491 / 0.35 (25799) hydrogen bonds : bond 0.04204 / 2.79 ( 912) hydrogen bonds : angle 4.25985 / 3.01 ( 2673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 600 time to evaluate : 0.757 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: K 320 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8724 (mp) REVERT: K 335 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7027 (tm) REVERT: K 362 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8454 (mt-10) REVERT: K 413 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: N 140 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7626 (tp30) REVERT: N 155 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8615 (tmtp) REVERT: N 180 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8250 (ttm-80) REVERT: N 206 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8693 (m) REVERT: N 224 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8031 (mtpp) REVERT: N 227 VAL cc_start: 0.8720 (p) cc_final: 0.8464 (m) REVERT: N 421 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7596 (tp-100) REVERT: N 424 GLN cc_start: 0.8141 (mt0) cc_final: 0.7708 (mt0) REVERT: N 489 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (mt) REVERT: N 595 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7712 (tm-30) REVERT: N 599 GLN cc_start: 0.8890 (mm110) cc_final: 0.8585 (mm110) REVERT: O 128 MET cc_start: 0.8670 (tmt) cc_final: 0.8031 (tmm) REVERT: O 133 ASP cc_start: 0.7347 (m-30) cc_final: 0.7054 (t0) REVERT: O 156 LYS cc_start: 0.8432 (ptmm) cc_final: 0.7885 (pttt) REVERT: O 169 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8528 (p0) REVERT: O 386 ASP cc_start: 0.7820 (p0) cc_final: 0.7504 (p0) REVERT: O 402 ASP cc_start: 0.7308 (t0) cc_final: 0.6838 (t0) REVERT: O 405 GLN cc_start: 0.8112 (mp10) cc_final: 0.7763 (mt0) REVERT: O 409 TYR cc_start: 0.8740 (t80) cc_final: 0.8331 (t80) REVERT: O 430 LYS cc_start: 0.8863 (tttt) cc_final: 0.8491 (tttt) REVERT: O 474 ASP cc_start: 0.8292 (t70) cc_final: 0.7572 (p0) REVERT: O 490 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8223 (mtmm) REVERT: O 494 ARG cc_start: 0.8278 (tmt170) cc_final: 0.8068 (tmt170) REVERT: O 568 GLU cc_start: 0.8122 (tp30) cc_final: 0.7533 (tp30) REVERT: O 571 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7869 (ttp80) REVERT: O 595 GLU cc_start: 0.7255 (tp30) cc_final: 0.6961 (tm-30) REVERT: O 603 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7878 (mpp-170) REVERT: O 607 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7280 (tpp80) REVERT: O 610 GLN cc_start: 0.8066 (pp30) cc_final: 0.7808 (pp30) REVERT: P 64 LEU cc_start: 0.8679 (mm) cc_final: 0.8373 (tp) REVERT: P 82 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8129 (tp30) REVERT: P 127 TYR cc_start: 0.6401 (t80) cc_final: 0.5168 (t80) REVERT: P 297 PHE cc_start: 0.7702 (m-80) cc_final: 0.7476 (m-80) REVERT: P 319 MET cc_start: 0.8085 (tmm) cc_final: 0.7673 (tmm) REVERT: P 399 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8012 (tp) REVERT: P 514 LYS cc_start: 0.6640 (ttmt) cc_final: 0.6179 (ttpt) REVERT: Q 286 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7132 (mm-30) REVERT: Q 312 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: Q 315 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7797 (tm-30) REVERT: Q 378 LYS cc_start: 0.8653 (tmmm) cc_final: 0.8437 (ttpp) REVERT: Q 395 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8264 (tmmt) REVERT: R 762 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7956 (tp30) REVERT: R 843 GLU cc_start: 0.8452 (tp30) cc_final: 0.7926 (tm-30) REVERT: R 845 GLN cc_start: 0.8216 (mp10) cc_final: 0.7780 (mp10) REVERT: R 847 ASP cc_start: 0.8322 (m-30) cc_final: 0.8047 (t0) REVERT: R 922 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7701 (tm-30) REVERT: R 946 ASN cc_start: 0.8483 (t0) cc_final: 0.8177 (t0) REVERT: R 952 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8144 (mtt) REVERT: R 1093 MET cc_start: 0.8107 (mtm) cc_final: 0.7188 (mpp) REVERT: R 1115 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8486 (p90) REVERT: R 1117 GLN cc_start: 0.8315 (mt0) cc_final: 0.8026 (mt0) REVERT: R 1131 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: R 1158 ASP cc_start: 0.8579 (m-30) cc_final: 0.8277 (m-30) REVERT: R 1160 LEU cc_start: 0.8759 (tt) cc_final: 0.8535 (tm) REVERT: R 1191 ASN cc_start: 0.8706 (p0) cc_final: 0.8059 (p0) REVERT: R 1218 ASP cc_start: 0.7762 (m-30) cc_final: 0.7548 (t0) REVERT: R 1230 VAL cc_start: 0.5364 (OUTLIER) cc_final: 0.4425 (t) REVERT: S 91 LYS cc_start: 0.8640 (tppt) cc_final: 0.8431 (tppt) REVERT: S 140 ASN cc_start: 0.8109 (m-40) cc_final: 0.7826 (m-40) REVERT: S 201 ASN cc_start: 0.8361 (t0) cc_final: 0.8069 (t0) REVERT: S 237 GLN cc_start: 0.8723 (tp40) cc_final: 0.8138 (tp40) REVERT: S 241 GLU cc_start: 0.7892 (pt0) cc_final: 0.7506 (pt0) REVERT: S 313 SER cc_start: 0.8948 (t) cc_final: 0.8519 (p) REVERT: S 334 THR cc_start: 0.8395 (m) cc_final: 0.7996 (p) REVERT: S 375 ASP cc_start: 0.8210 (t0) cc_final: 0.7582 (t0) REVERT: S 427 SER cc_start: 0.9088 (m) cc_final: 0.8817 (t) REVERT: S 442 GLU cc_start: 0.7989 (mp0) cc_final: 0.7600 (mp0) REVERT: T 361 THR cc_start: 0.6641 (m) cc_final: 0.5997 (m) REVERT: T 365 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8072 (tm-30) REVERT: T 392 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7882 (m-40) REVERT: U 71 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6603 (mm) REVERT: U 76 GLN cc_start: 0.8360 (mt0) cc_final: 0.8090 (mm-40) REVERT: U 83 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7915 (mtt180) outliers start: 91 outliers final: 34 residues processed: 647 average time/residue: 0.6956 time to fit residues: 498.8544 Evaluate side-chains 619 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 569 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 489 LEU Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 603 ARG Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 570 THR Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 285 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 401 MET Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 765 GLN Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 952 MET Chi-restraints excluded: chain R residue 987 GLN Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1131 GLU Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain R residue 1230 VAL Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain T residue 392 ASN Chi-restraints excluded: chain U residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 12 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 182 optimal weight: 0.0870 chunk 156 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 143 ASN N 203 ASN N 610 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 GLN P 136 ASN ** P 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 522 ASN Q 351 GLN Q 482 GLN R 830 HIS R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN 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 = 0.139509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.119667 restraints weight = 37216.420| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.04 r_work: 0.3613 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19079 Z= 0.170 Angle : 0.715 11.672 25799 Z= 0.358 Chirality : 0.042 0.177 2825 Planarity : 0.005 0.070 3403 Dihedral : 4.664 39.574 2571 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.65 % Allowed : 30.93 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.18), residues: 2293 helix: 1.32 (0.15), residues: 1233 sheet: -1.99 (0.49), residues: 103 loop : -1.95 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 112 TYR 0.031 0.002 TYR K 369 PHE 0.018 0.002 PHE S 358 TRP 0.041 0.002 TRP S 189 HIS 0.006 0.001 HIS P 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (19079) covalent geometry : angle 0.71479 / 0.36 (25799) hydrogen bonds : bond 0.04215 / 2.80 ( 912) hydrogen bonds : angle 4.24774 / 3.00 ( 2673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 593 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: K 320 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8714 (mp) REVERT: K 335 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7072 (tm) REVERT: K 358 LYS cc_start: 0.8357 (mmmm) cc_final: 0.7947 (mmmt) REVERT: K 413 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: N 140 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7402 (tp30) REVERT: N 155 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8612 (tmtp) REVERT: N 180 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: N 206 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8764 (m) REVERT: N 209 ASP cc_start: 0.8459 (t0) cc_final: 0.8177 (t0) REVERT: N 224 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8160 (mtpt) REVERT: N 421 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7604 (tp-100) REVERT: N 424 GLN cc_start: 0.8227 (mt0) cc_final: 0.7979 (mt0) REVERT: N 494 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7553 (ttm110) REVERT: N 595 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7703 (tm-30) REVERT: N 599 GLN cc_start: 0.8911 (mm110) cc_final: 0.8627 (mm110) REVERT: N 623 VAL cc_start: 0.8270 (t) cc_final: 0.7993 (p) REVERT: O 128 MET cc_start: 0.8736 (tmt) cc_final: 0.8076 (tmm) REVERT: O 133 ASP cc_start: 0.7433 (m-30) cc_final: 0.6871 (t0) REVERT: O 156 LYS cc_start: 0.8401 (ptmm) cc_final: 0.8011 (pttt) REVERT: O 394 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8228 (mp0) REVERT: O 402 ASP cc_start: 0.7317 (t0) cc_final: 0.6815 (t0) REVERT: O 405 GLN cc_start: 0.8155 (mp10) cc_final: 0.7732 (mt0) REVERT: O 409 TYR cc_start: 0.8802 (t80) cc_final: 0.8259 (t80) REVERT: O 430 LYS cc_start: 0.8852 (tttt) cc_final: 0.8476 (tttt) REVERT: O 474 ASP cc_start: 0.8244 (t70) cc_final: 0.7530 (p0) REVERT: O 490 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8220 (mtmm) REVERT: O 568 GLU cc_start: 0.8101 (tp30) cc_final: 0.7491 (tp30) REVERT: O 571 ARG cc_start: 0.8415 (ttp80) cc_final: 0.7893 (ttp80) REVERT: O 595 GLU cc_start: 0.7341 (tp30) cc_final: 0.7045 (tm-30) REVERT: O 603 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7901 (mpp-170) REVERT: O 607 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7322 (tpp80) REVERT: O 610 GLN cc_start: 0.8126 (pp30) cc_final: 0.7853 (pp30) REVERT: P 64 LEU cc_start: 0.8693 (mm) cc_final: 0.8389 (tp) REVERT: P 82 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8123 (tp30) REVERT: P 127 TYR cc_start: 0.6530 (t80) cc_final: 0.5296 (t80) REVERT: P 128 LYS cc_start: 0.7904 (tptp) cc_final: 0.7684 (tptp) REVERT: P 319 MET cc_start: 0.8076 (tmm) cc_final: 0.7584 (tmm) REVERT: P 399 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8070 (tp) REVERT: P 514 LYS cc_start: 0.6856 (ttmt) cc_final: 0.6398 (ttmt) REVERT: Q 286 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7196 (mt-10) REVERT: Q 300 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7456 (ttm170) REVERT: Q 312 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: Q 315 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7814 (tm-30) REVERT: Q 378 LYS cc_start: 0.8676 (tmmm) cc_final: 0.8476 (ttpp) REVERT: Q 395 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8286 (tmmt) REVERT: R 762 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7905 (tp30) REVERT: R 843 GLU cc_start: 0.8428 (tp30) cc_final: 0.7908 (tm-30) REVERT: R 845 GLN cc_start: 0.8258 (mp10) cc_final: 0.7846 (mp10) REVERT: R 847 ASP cc_start: 0.8299 (m-30) cc_final: 0.8033 (t0) REVERT: R 921 ASP cc_start: 0.8119 (t0) cc_final: 0.7855 (t0) REVERT: R 922 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7799 (tm-30) REVERT: R 946 ASN cc_start: 0.8463 (t0) cc_final: 0.8149 (t0) REVERT: R 952 MET cc_start: 0.8439 (mtp) cc_final: 0.8167 (mtt) REVERT: R 1115 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8527 (p90) REVERT: R 1117 GLN cc_start: 0.8382 (mt0) cc_final: 0.8166 (mt0) REVERT: R 1131 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: R 1158 ASP cc_start: 0.8602 (m-30) cc_final: 0.8302 (m-30) REVERT: R 1160 LEU cc_start: 0.8756 (tt) cc_final: 0.8533 (tm) REVERT: R 1191 ASN cc_start: 0.8736 (p0) cc_final: 0.8109 (p0) REVERT: R 1218 ASP cc_start: 0.7817 (m-30) cc_final: 0.7591 (t0) REVERT: S 91 LYS cc_start: 0.8673 (tppt) cc_final: 0.8427 (tppt) REVERT: S 96 ARG cc_start: 0.7124 (mmp80) cc_final: 0.6780 (mmp80) REVERT: S 99 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7298 (ttp-110) REVERT: S 140 ASN cc_start: 0.8091 (m-40) cc_final: 0.7828 (m-40) REVERT: S 201 ASN cc_start: 0.8394 (t0) cc_final: 0.8110 (t0) REVERT: S 303 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7846 (tm-30) REVERT: S 313 SER cc_start: 0.8913 (t) cc_final: 0.8534 (p) REVERT: S 334 THR cc_start: 0.8377 (m) cc_final: 0.7978 (p) REVERT: S 375 ASP cc_start: 0.8261 (t0) cc_final: 0.7634 (t0) REVERT: S 427 SER cc_start: 0.9093 (m) cc_final: 0.8827 (t) REVERT: S 442 GLU cc_start: 0.8019 (mp0) cc_final: 0.7607 (mp0) REVERT: T 361 THR cc_start: 0.6682 (m) cc_final: 0.6104 (m) REVERT: T 365 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8062 (tm-30) REVERT: T 390 TYR cc_start: 0.8298 (t80) cc_final: 0.7855 (t80) REVERT: T 392 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: U 71 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6577 (mm) REVERT: U 76 GLN cc_start: 0.8384 (mt0) cc_final: 0.8104 (mm-40) REVERT: U 83 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7819 (mpt-90) outliers start: 93 outliers final: 51 residues processed: 638 average time/residue: 0.7135 time to fit residues: 503.2990 Evaluate side-chains 634 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 570 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 400 ARG Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 142 PHE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 617 LEU Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 210 ASP Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 570 THR Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 167 ILE Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 401 MET Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 765 GLN Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 856 THR Chi-restraints excluded: chain R residue 859 GLU Chi-restraints excluded: chain R residue 944 THR Chi-restraints excluded: chain R residue 987 GLN Chi-restraints excluded: chain R residue 997 LEU Chi-restraints excluded: chain R residue 1007 HIS Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1131 GLU Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 392 ASN Chi-restraints excluded: chain U residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 113 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 165 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 163 optimal weight: 0.1980 chunk 145 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 184 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 203 ASN N 610 GLN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 GLN ** P 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 830 HIS R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN ** T 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.140222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.120364 restraints weight = 37499.355| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.06 r_work: 0.3619 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19079 Z= 0.156 Angle : 0.729 11.568 25799 Z= 0.366 Chirality : 0.042 0.211 2825 Planarity : 0.005 0.070 3403 Dihedral : 4.685 39.954 2571 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.40 % Allowed : 32.03 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2293 helix: 1.33 (0.15), residues: 1233 sheet: -1.43 (0.54), residues: 88 loop : -1.93 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 147 TYR 0.036 0.002 TYR K 369 PHE 0.032 0.002 PHE P 297 TRP 0.045 0.002 TRP S 189 HIS 0.006 0.001 HIS R 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (19079) covalent geometry : angle 0.72898 / 0.37 (25799) hydrogen bonds : bond 0.04076 / 2.71 ( 912) hydrogen bonds : angle 4.22871 / 2.97 ( 2673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 582 time to evaluate : 0.832 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: K 311 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7766 (mm-30) REVERT: K 320 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8733 (mp) REVERT: K 358 LYS cc_start: 0.8383 (mmmm) cc_final: 0.7976 (mmmt) REVERT: K 407 ARG cc_start: 0.8232 (tmm160) cc_final: 0.7865 (tmm-80) REVERT: K 413 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: N 140 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7429 (tp30) REVERT: N 155 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8558 (tmtp) REVERT: N 180 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8241 (ttm-80) REVERT: N 206 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8771 (m) REVERT: N 209 ASP cc_start: 0.8406 (t0) cc_final: 0.8134 (t0) REVERT: N 224 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8112 (mtpt) REVERT: N 227 VAL cc_start: 0.8700 (p) cc_final: 0.8460 (m) REVERT: N 421 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7596 (tp-100) REVERT: N 424 GLN cc_start: 0.8224 (mt0) cc_final: 0.7774 (mt0) REVERT: N 489 LEU cc_start: 0.8853 (mt) cc_final: 0.8582 (mt) REVERT: N 494 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7542 (ttm110) REVERT: N 595 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7685 (tm-30) REVERT: N 599 GLN cc_start: 0.8866 (mm110) cc_final: 0.8555 (mm110) REVERT: N 623 VAL cc_start: 0.8326 (t) cc_final: 0.8080 (p) REVERT: O 128 MET cc_start: 0.8725 (tmt) cc_final: 0.8078 (tmm) REVERT: O 133 ASP cc_start: 0.7456 (m-30) cc_final: 0.7196 (t0) REVERT: O 156 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8192 (pttt) REVERT: O 169 ASN cc_start: 0.8668 (p0) cc_final: 0.8444 (p0) REVERT: O 386 ASP cc_start: 0.8221 (p0) cc_final: 0.7988 (p0) REVERT: O 394 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8227 (mp0) REVERT: O 402 ASP cc_start: 0.7256 (t0) cc_final: 0.6986 (t0) REVERT: O 409 TYR cc_start: 0.8781 (t80) cc_final: 0.8234 (t80) REVERT: O 430 LYS cc_start: 0.8840 (tttt) cc_final: 0.8482 (tttt) REVERT: O 490 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8234 (mtmm) REVERT: O 568 GLU cc_start: 0.8108 (tp30) cc_final: 0.7468 (tp30) REVERT: O 570 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8436 (t) REVERT: O 571 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7892 (ttp80) REVERT: O 595 GLU cc_start: 0.7324 (tp30) cc_final: 0.7018 (tm-30) REVERT: O 603 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7923 (mpp-170) REVERT: O 607 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7300 (tpp80) REVERT: O 610 GLN cc_start: 0.8143 (pp30) cc_final: 0.7872 (pp30) REVERT: P 64 LEU cc_start: 0.8700 (mm) cc_final: 0.8396 (tp) REVERT: P 82 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8132 (tp30) REVERT: P 127 TYR cc_start: 0.6549 (t80) cc_final: 0.5300 (t80) REVERT: P 128 LYS cc_start: 0.7875 (tptp) cc_final: 0.7668 (tptp) REVERT: P 319 MET cc_start: 0.8112 (tmm) cc_final: 0.7588 (tmm) REVERT: P 359 LEU cc_start: 0.8708 (tm) cc_final: 0.8495 (tt) REVERT: P 514 LYS cc_start: 0.6797 (ttmt) cc_final: 0.6245 (ttmt) REVERT: Q 286 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7200 (mm-30) REVERT: Q 312 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: Q 315 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7855 (tm-30) REVERT: Q 395 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8265 (tmmt) REVERT: R 843 GLU cc_start: 0.8465 (tp30) cc_final: 0.7958 (tm-30) REVERT: R 845 GLN cc_start: 0.8255 (mp10) cc_final: 0.7846 (mp10) REVERT: R 847 ASP cc_start: 0.8290 (m-30) cc_final: 0.8030 (t0) REVERT: R 921 ASP cc_start: 0.8110 (t0) cc_final: 0.7850 (t0) REVERT: R 922 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7139 (tm-30) REVERT: R 926 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8099 (mttt) REVERT: R 946 ASN cc_start: 0.8465 (t0) cc_final: 0.8150 (t0) REVERT: R 952 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: R 1115 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8517 (p90) REVERT: R 1117 GLN cc_start: 0.8373 (mt0) cc_final: 0.8141 (mt0) REVERT: R 1158 ASP cc_start: 0.8604 (m-30) cc_final: 0.8302 (m-30) REVERT: R 1160 LEU cc_start: 0.8740 (tt) cc_final: 0.8511 (tm) REVERT: R 1191 ASN cc_start: 0.8732 (p0) cc_final: 0.8068 (p0) REVERT: R 1218 ASP cc_start: 0.7814 (m-30) cc_final: 0.7603 (t0) REVERT: R 1230 VAL cc_start: 0.5336 (OUTLIER) cc_final: 0.4319 (t) REVERT: S 91 LYS cc_start: 0.8672 (tppt) cc_final: 0.8464 (tppt) REVERT: S 96 ARG cc_start: 0.7161 (mmp80) cc_final: 0.6606 (mmp80) REVERT: S 99 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.6932 (ttp-110) REVERT: S 140 ASN cc_start: 0.8108 (m-40) cc_final: 0.7841 (m-40) REVERT: S 201 ASN cc_start: 0.8411 (t0) cc_final: 0.8126 (t0) REVERT: S 237 GLN cc_start: 0.8627 (tp40) cc_final: 0.8236 (tp40) REVERT: S 241 GLU cc_start: 0.8081 (pt0) cc_final: 0.7418 (pt0) REVERT: S 313 SER cc_start: 0.8909 (t) cc_final: 0.8508 (p) REVERT: S 334 THR cc_start: 0.8356 (m) cc_final: 0.7967 (p) REVERT: S 375 ASP cc_start: 0.8246 (t0) cc_final: 0.7649 (t0) REVERT: S 427 SER cc_start: 0.9102 (m) cc_final: 0.8844 (t) REVERT: S 442 GLU cc_start: 0.8006 (mp0) cc_final: 0.7562 (mp0) REVERT: T 361 THR cc_start: 0.6582 (m) cc_final: 0.6061 (m) REVERT: T 365 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8076 (tm-30) REVERT: T 386 MET cc_start: 0.8275 (mpp) cc_final: 0.7829 (pmm) REVERT: T 390 TYR cc_start: 0.8239 (t80) cc_final: 0.7835 (t80) REVERT: T 392 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7929 (m-40) REVERT: U 71 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6663 (mm) REVERT: U 76 GLN cc_start: 0.8397 (mt0) cc_final: 0.8128 (mm-40) outliers start: 88 outliers final: 49 residues processed: 626 average time/residue: 0.7008 time to fit residues: 485.7798 Evaluate side-chains 622 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 560 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 142 PHE Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 593 GLU Chi-restraints excluded: chain N residue 603 ARG Chi-restraints excluded: chain N residue 617 LEU Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 659 ASN Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 206 GLN Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 570 THR Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain O residue 607 ARG Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 401 MET Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 765 GLN Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 952 MET Chi-restraints excluded: chain R residue 987 GLN Chi-restraints excluded: chain R residue 997 LEU Chi-restraints excluded: chain R residue 1093 MET Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1124 ARG Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain R residue 1230 VAL Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 274 LEU Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 381 TYR Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain S residue 439 THR Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 392 ASN Chi-restraints excluded: chain U residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 207 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 404 HIS N 143 ASN N 203 ASN N 610 GLN O 169 ASN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 GLN ** P 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 351 GLN R 830 HIS R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN ** T 381 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.139948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120223 restraints weight = 37330.802| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.06 r_work: 0.3616 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19079 Z= 0.165 Angle : 0.732 10.218 25799 Z= 0.370 Chirality : 0.042 0.164 2825 Planarity : 0.005 0.056 3403 Dihedral : 4.703 41.291 2571 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.65 % Allowed : 31.88 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2293 helix: 1.36 (0.15), residues: 1232 sheet: -1.63 (0.53), residues: 97 loop : -1.94 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 458 TYR 0.037 0.002 TYR K 369 PHE 0.021 0.002 PHE P 224 TRP 0.054 0.003 TRP S 189 HIS 0.007 0.001 HIS R 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (19079) covalent geometry : angle 0.73208 / 0.37 (25799) hydrogen bonds : bond 0.04047 / 2.70 ( 912) hydrogen bonds : angle 4.21003 / 2.95 ( 2673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 579 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 311 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7788 (mm-30) REVERT: K 320 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8714 (mp) REVERT: K 335 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7112 (tm) REVERT: K 413 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: N 155 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8574 (tmtp) REVERT: N 180 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8187 (ttm-80) REVERT: N 206 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8768 (m) REVERT: N 209 ASP cc_start: 0.8392 (t0) cc_final: 0.8128 (t0) REVERT: N 224 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8108 (mtpt) REVERT: N 421 GLN cc_start: 0.8542 (mm-40) cc_final: 0.7575 (tp-100) REVERT: N 424 GLN cc_start: 0.8215 (mt0) cc_final: 0.7934 (mt0) REVERT: N 494 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7535 (ttm110) REVERT: N 595 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7677 (tm-30) REVERT: N 599 GLN cc_start: 0.8858 (mm110) cc_final: 0.8576 (mm110) REVERT: N 606 GLU cc_start: 0.8425 (tp30) cc_final: 0.8223 (tp30) REVERT: N 623 VAL cc_start: 0.8360 (t) cc_final: 0.8116 (p) REVERT: O 128 MET cc_start: 0.8755 (tmt) cc_final: 0.8115 (tmm) REVERT: O 133 ASP cc_start: 0.7482 (m-30) cc_final: 0.7179 (t0) REVERT: O 156 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8119 (pttt) REVERT: O 386 ASP cc_start: 0.8184 (p0) cc_final: 0.7873 (p0) REVERT: O 402 ASP cc_start: 0.7210 (t0) cc_final: 0.6952 (t0) REVERT: O 409 TYR cc_start: 0.8750 (t80) cc_final: 0.8178 (t80) REVERT: O 430 LYS cc_start: 0.8843 (tttt) cc_final: 0.8495 (tttt) REVERT: O 490 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8255 (mtmm) REVERT: O 568 GLU cc_start: 0.8116 (tp30) cc_final: 0.7895 (tp30) REVERT: O 570 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8423 (t) REVERT: O 603 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7935 (mpp-170) REVERT: O 607 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7442 (tpp80) REVERT: O 610 GLN cc_start: 0.8153 (pp30) cc_final: 0.7869 (pp30) REVERT: P 64 LEU cc_start: 0.8693 (mm) cc_final: 0.8405 (tp) REVERT: P 71 LYS cc_start: 0.8932 (tppp) cc_final: 0.8625 (tppp) REVERT: P 82 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8115 (tp30) REVERT: P 127 TYR cc_start: 0.6537 (t80) cc_final: 0.5290 (t80) REVERT: P 250 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7124 (p90) REVERT: P 319 MET cc_start: 0.8093 (tmm) cc_final: 0.7553 (tmm) REVERT: P 359 LEU cc_start: 0.8731 (tm) cc_final: 0.8512 (tt) REVERT: Q 286 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7198 (mm-30) REVERT: Q 312 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: Q 315 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7784 (tm-30) REVERT: Q 378 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8399 (pttm) REVERT: Q 395 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8273 (tmmt) REVERT: R 762 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7806 (mm-30) REVERT: R 843 GLU cc_start: 0.8477 (tp30) cc_final: 0.7972 (tm-30) REVERT: R 845 GLN cc_start: 0.8244 (mp10) cc_final: 0.7832 (mp10) REVERT: R 847 ASP cc_start: 0.8293 (m-30) cc_final: 0.8034 (t0) REVERT: R 897 ASP cc_start: 0.8058 (t0) cc_final: 0.7835 (t0) REVERT: R 921 ASP cc_start: 0.8144 (t0) cc_final: 0.7869 (t0) REVERT: R 922 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7035 (tm-30) REVERT: R 926 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8060 (mttt) REVERT: R 946 ASN cc_start: 0.8357 (t0) cc_final: 0.8043 (t0) REVERT: R 952 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: R 967 GLU cc_start: 0.7875 (mp0) cc_final: 0.7651 (mp0) REVERT: R 1115 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8564 (p90) REVERT: R 1117 GLN cc_start: 0.8378 (mt0) cc_final: 0.8152 (mt0) REVERT: R 1131 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: R 1158 ASP cc_start: 0.8598 (m-30) cc_final: 0.8291 (m-30) REVERT: R 1160 LEU cc_start: 0.8769 (tt) cc_final: 0.8547 (tm) REVERT: R 1191 ASN cc_start: 0.8746 (p0) cc_final: 0.8074 (p0) REVERT: R 1218 ASP cc_start: 0.7797 (m-30) cc_final: 0.7507 (t0) REVERT: R 1230 VAL cc_start: 0.5386 (OUTLIER) cc_final: 0.4574 (t) REVERT: S 99 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7121 (ttp80) REVERT: S 140 ASN cc_start: 0.8115 (m-40) cc_final: 0.7856 (m-40) REVERT: S 201 ASN cc_start: 0.8406 (t0) cc_final: 0.8151 (t0) REVERT: S 237 GLN cc_start: 0.8704 (tp40) cc_final: 0.8347 (tp40) REVERT: S 241 GLU cc_start: 0.8104 (pt0) cc_final: 0.7682 (pt0) REVERT: S 300 SER cc_start: 0.7746 (m) cc_final: 0.7324 (p) REVERT: S 313 SER cc_start: 0.8864 (t) cc_final: 0.8360 (p) REVERT: S 334 THR cc_start: 0.8349 (m) cc_final: 0.7965 (p) REVERT: S 375 ASP cc_start: 0.8276 (t0) cc_final: 0.7671 (t0) REVERT: S 424 ILE cc_start: 0.8241 (mt) cc_final: 0.8036 (mm) REVERT: S 427 SER cc_start: 0.9107 (m) cc_final: 0.8846 (t) REVERT: S 442 GLU cc_start: 0.7978 (mp0) cc_final: 0.7600 (mp0) REVERT: T 361 THR cc_start: 0.6558 (m) cc_final: 0.6046 (m) REVERT: T 365 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8114 (tm-30) REVERT: T 377 ASN cc_start: 0.8782 (t0) cc_final: 0.8561 (t160) REVERT: T 381 ASN cc_start: 0.8477 (m110) cc_final: 0.8231 (p0) REVERT: T 386 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7881 (pmm) REVERT: T 390 TYR cc_start: 0.8281 (t80) cc_final: 0.7829 (t80) REVERT: U 71 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6672 (mm) REVERT: U 76 GLN cc_start: 0.8412 (mt0) cc_final: 0.8139 (mm-40) outliers start: 93 outliers final: 50 residues processed: 619 average time/residue: 0.6900 time to fit residues: 472.4456 Evaluate side-chains 624 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 557 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 400 ARG Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 155 LYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 603 ARG Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain N residue 648 VAL Chi-restraints excluded: chain N residue 659 ASN Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 206 GLN Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 570 THR Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain O residue 607 ARG Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 250 TRP Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 401 MET Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 765 GLN Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 887 THR Chi-restraints excluded: chain R residue 952 MET Chi-restraints excluded: chain R residue 987 GLN Chi-restraints excluded: chain R residue 1007 HIS Chi-restraints excluded: chain R residue 1093 MET Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1124 ARG Chi-restraints excluded: chain R residue 1131 GLU Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain R residue 1230 VAL Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 240 HIS Chi-restraints excluded: chain S residue 274 LEU Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain S residue 439 THR Chi-restraints excluded: chain T residue 386 MET Chi-restraints excluded: chain U residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 3 optimal weight: 0.2980 chunk 163 optimal weight: 0.0770 chunk 84 optimal weight: 0.0870 chunk 190 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 404 HIS N 203 ASN N 610 GLN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 GLN ** P 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 522 ASN R 830 HIS R 881 ASN R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN S 120 ASN ** T 381 ASN ** 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 = 0.4062 r_free = 0.4062 target = 0.141210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121444 restraints weight = 37179.195| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.05 r_work: 0.3640 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19079 Z= 0.147 Angle : 0.755 11.456 25799 Z= 0.380 Chirality : 0.042 0.212 2825 Planarity : 0.005 0.087 3403 Dihedral : 4.675 40.796 2571 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.20 % Allowed : 32.93 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.18), residues: 2293 helix: 1.42 (0.15), residues: 1227 sheet: -1.76 (0.52), residues: 103 loop : -1.86 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 112 TYR 0.040 0.002 TYR K 369 PHE 0.019 0.002 PHE P 224 TRP 0.058 0.002 TRP S 189 HIS 0.006 0.001 HIS R 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (19079) covalent geometry : angle 0.75497 / 0.38 (25799) hydrogen bonds : bond 0.03964 / 2.63 ( 912) hydrogen bonds : angle 4.20955 / 2.94 ( 2673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 569 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 311 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7748 (mm-30) REVERT: K 320 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8711 (mp) REVERT: K 358 LYS cc_start: 0.8412 (mmmm) cc_final: 0.7945 (mmmt) REVERT: K 413 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7171 (pt0) REVERT: N 206 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8762 (m) REVERT: N 224 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8072 (mtpt) REVERT: N 227 VAL cc_start: 0.8614 (p) cc_final: 0.8392 (m) REVERT: N 421 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7576 (tp-100) REVERT: N 424 GLN cc_start: 0.8188 (mt0) cc_final: 0.7878 (mt0) REVERT: N 595 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7665 (tm-30) REVERT: N 599 GLN cc_start: 0.8879 (mm110) cc_final: 0.8607 (mm110) REVERT: N 617 LEU cc_start: 0.6914 (tp) cc_final: 0.6679 (tt) REVERT: N 623 VAL cc_start: 0.8335 (t) cc_final: 0.8113 (p) REVERT: O 128 MET cc_start: 0.8733 (tmt) cc_final: 0.8184 (tmm) REVERT: O 133 ASP cc_start: 0.7432 (m-30) cc_final: 0.7114 (t0) REVERT: O 156 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8161 (pttt) REVERT: O 386 ASP cc_start: 0.8176 (p0) cc_final: 0.7922 (p0) REVERT: O 402 ASP cc_start: 0.7106 (t0) cc_final: 0.6836 (t0) REVERT: O 408 GLU cc_start: 0.8237 (tp30) cc_final: 0.7964 (tp30) REVERT: O 409 TYR cc_start: 0.8749 (t80) cc_final: 0.8334 (t80) REVERT: O 417 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7341 (mt-10) REVERT: O 430 LYS cc_start: 0.8823 (tttt) cc_final: 0.8494 (tttt) REVERT: O 474 ASP cc_start: 0.8189 (t70) cc_final: 0.7621 (p0) REVERT: O 490 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8200 (mtmm) REVERT: O 568 GLU cc_start: 0.8073 (tp30) cc_final: 0.7871 (tp30) REVERT: O 570 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8396 (t) REVERT: O 603 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7894 (mpp-170) REVERT: O 610 GLN cc_start: 0.8148 (pp30) cc_final: 0.7863 (pp30) REVERT: P 64 LEU cc_start: 0.8684 (mm) cc_final: 0.8409 (tp) REVERT: P 71 LYS cc_start: 0.8949 (tppp) cc_final: 0.8646 (tppp) REVERT: P 82 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8153 (tp30) REVERT: P 102 GLU cc_start: 0.7937 (tt0) cc_final: 0.7572 (tm-30) REVERT: P 127 TYR cc_start: 0.6582 (t80) cc_final: 0.5314 (t80) REVERT: P 319 MET cc_start: 0.8069 (tmm) cc_final: 0.7521 (tmm) REVERT: P 359 LEU cc_start: 0.8687 (tm) cc_final: 0.8463 (tt) REVERT: P 394 TYR cc_start: 0.1229 (m-10) cc_final: 0.0949 (m-10) REVERT: P 427 LYS cc_start: 0.8530 (mptt) cc_final: 0.8147 (mppt) REVERT: P 514 LYS cc_start: 0.6637 (ttmt) cc_final: 0.6223 (ttpt) REVERT: Q 286 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7282 (mm-30) REVERT: Q 312 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: Q 315 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7735 (tm-30) REVERT: Q 378 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8336 (pttm) REVERT: Q 395 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8271 (tmmt) REVERT: R 762 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7769 (mm-30) REVERT: R 843 GLU cc_start: 0.8466 (tp30) cc_final: 0.7955 (tm-30) REVERT: R 845 GLN cc_start: 0.8233 (mp10) cc_final: 0.7825 (mp10) REVERT: R 847 ASP cc_start: 0.8308 (m-30) cc_final: 0.8094 (t0) REVERT: R 897 ASP cc_start: 0.8053 (t0) cc_final: 0.7811 (t0) REVERT: R 921 ASP cc_start: 0.8101 (t0) cc_final: 0.7814 (t0) REVERT: R 922 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7755 (tm-30) REVERT: R 940 MET cc_start: 0.8745 (mmm) cc_final: 0.8493 (tpp) REVERT: R 946 ASN cc_start: 0.8300 (t0) cc_final: 0.8024 (t0) REVERT: R 952 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8007 (mtt) REVERT: R 1115 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8524 (p90) REVERT: R 1117 GLN cc_start: 0.8369 (mt0) cc_final: 0.8167 (mt0) REVERT: R 1131 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: R 1158 ASP cc_start: 0.8595 (m-30) cc_final: 0.8289 (m-30) REVERT: R 1160 LEU cc_start: 0.8751 (tt) cc_final: 0.8534 (tm) REVERT: R 1191 ASN cc_start: 0.8751 (p0) cc_final: 0.8037 (p0) REVERT: R 1218 ASP cc_start: 0.7811 (m-30) cc_final: 0.7539 (t0) REVERT: S 99 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7613 (ttp-110) REVERT: S 118 TYR cc_start: 0.8649 (m-10) cc_final: 0.8440 (m-10) REVERT: S 140 ASN cc_start: 0.8020 (m-40) cc_final: 0.7753 (m-40) REVERT: S 201 ASN cc_start: 0.8378 (t0) cc_final: 0.8095 (t0) REVERT: S 237 GLN cc_start: 0.8712 (tp40) cc_final: 0.8365 (tp40) REVERT: S 300 SER cc_start: 0.7761 (m) cc_final: 0.7230 (p) REVERT: S 303 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7771 (pp20) REVERT: S 313 SER cc_start: 0.8888 (t) cc_final: 0.8459 (p) REVERT: S 334 THR cc_start: 0.8362 (m) cc_final: 0.7970 (p) REVERT: S 375 ASP cc_start: 0.8256 (t0) cc_final: 0.7644 (t0) REVERT: S 427 SER cc_start: 0.9085 (m) cc_final: 0.8835 (t) REVERT: T 361 THR cc_start: 0.6892 (m) cc_final: 0.6411 (m) REVERT: T 365 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8130 (tm-30) REVERT: T 377 ASN cc_start: 0.8773 (t0) cc_final: 0.8546 (t160) REVERT: T 381 ASN cc_start: 0.8491 (m110) cc_final: 0.8218 (p0) REVERT: T 386 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7879 (pmm) REVERT: T 390 TYR cc_start: 0.8340 (t80) cc_final: 0.7890 (t80) REVERT: U 71 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6644 (mm) REVERT: U 76 GLN cc_start: 0.8401 (mt0) cc_final: 0.8180 (mm-40) REVERT: U 83 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8072 (mpt-90) outliers start: 84 outliers final: 41 residues processed: 609 average time/residue: 0.6933 time to fit residues: 468.4326 Evaluate side-chains 605 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 551 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 400 ARG Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 603 ARG Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain N residue 659 ASN Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 570 THR Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 603 ARG Chi-restraints excluded: chain O residue 607 ARG Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 312 GLU Chi-restraints excluded: chain Q residue 401 MET Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 952 MET Chi-restraints excluded: chain R residue 987 GLN Chi-restraints excluded: chain R residue 1093 MET Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1124 ARG Chi-restraints excluded: chain R residue 1131 GLU Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 274 LEU Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain S residue 439 THR Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 386 MET Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 84 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 67 optimal weight: 0.0270 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 404 HIS N 203 ASN N 610 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 GLN ** P 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 360 ASN Q 351 GLN R 830 HIS R 915 ASN ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1070 HIS ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 72 ASN S 80 GLN S 120 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.139888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.120125 restraints weight = 37292.533| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.05 r_work: 0.3624 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19079 Z= 0.173 Angle : 0.799 15.761 25799 Z= 0.401 Chirality : 0.043 0.200 2825 Planarity : 0.005 0.069 3403 Dihedral : 4.727 42.224 2571 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.40 % Allowed : 34.43 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.18), residues: 2293 helix: 1.35 (0.15), residues: 1232 sheet: -1.41 (0.56), residues: 99 loop : -1.89 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 112 TYR 0.038 0.002 TYR K 369 PHE 0.043 0.002 PHE S 333 TRP 0.058 0.003 TRP S 189 HIS 0.007 0.001 HIS R 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (19079) covalent geometry : angle 0.79916 / 0.40 (25799) hydrogen bonds : bond 0.04058 / 2.69 ( 912) hydrogen bonds : angle 4.25543 / 2.96 ( 2673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 554 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 311 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7771 (mm-30) REVERT: K 320 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8700 (mp) REVERT: K 358 LYS cc_start: 0.8425 (mmmm) cc_final: 0.7977 (mmmt) REVERT: K 413 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: N 206 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8809 (m) REVERT: N 224 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7938 (mtpp) REVERT: N 227 VAL cc_start: 0.8606 (p) cc_final: 0.8377 (m) REVERT: N 421 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7726 (tp-100) REVERT: N 424 GLN cc_start: 0.8186 (mt0) cc_final: 0.7768 (mt0) REVERT: N 494 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7502 (ttp80) REVERT: N 595 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7661 (tm-30) REVERT: N 599 GLN cc_start: 0.8899 (mm110) cc_final: 0.8651 (mm110) REVERT: N 614 LEU cc_start: 0.7085 (pp) cc_final: 0.6784 (pp) REVERT: N 623 VAL cc_start: 0.8337 (t) cc_final: 0.8120 (p) REVERT: N 661 MET cc_start: 0.5464 (ppp) cc_final: 0.4119 (ptp) REVERT: O 128 MET cc_start: 0.8749 (tmt) cc_final: 0.8220 (tmm) REVERT: O 133 ASP cc_start: 0.7490 (m-30) cc_final: 0.7174 (t0) REVERT: O 156 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8227 (pttt) REVERT: O 175 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.6953 (p) REVERT: O 182 ASN cc_start: 0.7969 (m110) cc_final: 0.7639 (m-40) REVERT: O 386 ASP cc_start: 0.8205 (p0) cc_final: 0.7983 (p0) REVERT: O 402 ASP cc_start: 0.7133 (t0) cc_final: 0.6852 (t0) REVERT: O 408 GLU cc_start: 0.8280 (tp30) cc_final: 0.7939 (tp30) REVERT: O 409 TYR cc_start: 0.8771 (t80) cc_final: 0.8293 (t80) REVERT: O 417 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6954 (mp0) REVERT: O 430 LYS cc_start: 0.8846 (tttt) cc_final: 0.8512 (tttt) REVERT: O 445 MET cc_start: 0.7861 (mmm) cc_final: 0.7629 (tpt) REVERT: O 490 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: O 568 GLU cc_start: 0.8075 (tp30) cc_final: 0.7870 (tp30) REVERT: O 570 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8402 (t) REVERT: O 594 MET cc_start: 0.6779 (tpp) cc_final: 0.6545 (tpt) REVERT: O 610 GLN cc_start: 0.8185 (pp30) cc_final: 0.7893 (pp30) REVERT: P 64 LEU cc_start: 0.8712 (mm) cc_final: 0.8404 (tp) REVERT: P 69 SER cc_start: 0.8712 (m) cc_final: 0.8257 (p) REVERT: P 71 LYS cc_start: 0.8942 (tppp) cc_final: 0.8655 (tppp) REVERT: P 82 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8131 (tp30) REVERT: P 127 TYR cc_start: 0.6630 (t80) cc_final: 0.5384 (t80) REVERT: P 319 MET cc_start: 0.8047 (tmm) cc_final: 0.7513 (tmm) REVERT: P 359 LEU cc_start: 0.8731 (tm) cc_final: 0.8503 (tt) REVERT: P 514 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6289 (ttpt) REVERT: Q 286 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7289 (mm-30) REVERT: Q 315 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7744 (tm-30) REVERT: Q 395 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8268 (tmmt) REVERT: R 762 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7789 (mm-30) REVERT: R 843 GLU cc_start: 0.8464 (tp30) cc_final: 0.7948 (tm-30) REVERT: R 845 GLN cc_start: 0.8256 (mp10) cc_final: 0.7830 (mp10) REVERT: R 847 ASP cc_start: 0.8352 (m-30) cc_final: 0.8148 (t0) REVERT: R 897 ASP cc_start: 0.8056 (t0) cc_final: 0.7843 (t0) REVERT: R 921 ASP cc_start: 0.8126 (t0) cc_final: 0.7839 (t0) REVERT: R 922 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7814 (tm-30) REVERT: R 946 ASN cc_start: 0.8323 (t0) cc_final: 0.8032 (t0) REVERT: R 1115 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8554 (p90) REVERT: R 1117 GLN cc_start: 0.8367 (mt0) cc_final: 0.8151 (mt0) REVERT: R 1158 ASP cc_start: 0.8609 (m-30) cc_final: 0.8296 (m-30) REVERT: R 1160 LEU cc_start: 0.8757 (tt) cc_final: 0.8529 (tm) REVERT: R 1191 ASN cc_start: 0.8762 (p0) cc_final: 0.8051 (p0) REVERT: R 1218 ASP cc_start: 0.7847 (m-30) cc_final: 0.7589 (t0) REVERT: S 99 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7657 (ttp-110) REVERT: S 118 TYR cc_start: 0.8684 (m-10) cc_final: 0.8480 (m-10) REVERT: S 140 ASN cc_start: 0.8023 (m-40) cc_final: 0.7779 (m-40) REVERT: S 201 ASN cc_start: 0.8391 (t0) cc_final: 0.8137 (t0) REVERT: S 237 GLN cc_start: 0.8729 (tp40) cc_final: 0.8378 (tp40) REVERT: S 300 SER cc_start: 0.7829 (m) cc_final: 0.7147 (p) REVERT: S 303 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7666 (pp20) REVERT: S 313 SER cc_start: 0.8865 (t) cc_final: 0.8477 (p) REVERT: S 375 ASP cc_start: 0.8249 (t0) cc_final: 0.7652 (t0) REVERT: S 424 ILE cc_start: 0.8247 (mt) cc_final: 0.8039 (mm) REVERT: S 427 SER cc_start: 0.9095 (m) cc_final: 0.8851 (t) REVERT: T 361 THR cc_start: 0.6582 (m) cc_final: 0.6121 (m) REVERT: T 365 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8149 (tm-30) REVERT: T 386 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7869 (pmm) REVERT: T 390 TYR cc_start: 0.8336 (t80) cc_final: 0.7889 (t80) REVERT: U 71 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6695 (mm) REVERT: U 76 GLN cc_start: 0.8404 (mt0) cc_final: 0.8160 (mm-40) REVERT: U 83 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8086 (mpt-90) outliers start: 68 outliers final: 38 residues processed: 584 average time/residue: 0.6943 time to fit residues: 449.5709 Evaluate side-chains 596 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 547 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 400 ARG Chi-restraints excluded: chain K residue 413 GLU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 589 LYS Chi-restraints excluded: chain N residue 626 VAL Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 490 LYS Chi-restraints excluded: chain O residue 570 THR Chi-restraints excluded: chain O residue 579 VAL Chi-restraints excluded: chain O residue 607 ARG Chi-restraints excluded: chain P residue 113 ARG Chi-restraints excluded: chain P residue 223 PHE Chi-restraints excluded: chain P residue 426 LEU Chi-restraints excluded: chain P residue 508 GLU Chi-restraints excluded: chain Q residue 311 HIS Chi-restraints excluded: chain Q residue 401 MET Chi-restraints excluded: chain Q residue 413 GLN Chi-restraints excluded: chain Q residue 420 PHE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain R residue 740 VAL Chi-restraints excluded: chain R residue 752 HIS Chi-restraints excluded: chain R residue 823 VAL Chi-restraints excluded: chain R residue 987 GLN Chi-restraints excluded: chain R residue 1093 MET Chi-restraints excluded: chain R residue 1115 PHE Chi-restraints excluded: chain R residue 1124 ARG Chi-restraints excluded: chain R residue 1132 THR Chi-restraints excluded: chain R residue 1225 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain S residue 290 PHE Chi-restraints excluded: chain S residue 428 ILE Chi-restraints excluded: chain S residue 430 SER Chi-restraints excluded: chain T residue 358 ILE Chi-restraints excluded: chain T residue 386 MET Chi-restraints excluded: chain T residue 394 ILE Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 56 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 182 optimal weight: 0.2980 chunk 159 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 203 ASN N 610 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 GLN ** P 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 360 ASN P 522 ASN R 830 HIS ** R1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1129 GLN S 80 GLN S 120 ASN ** S 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 176 GLN ** S 295 ASN ** 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 = 0.4038 r_free = 0.4038 target = 0.139091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119449 restraints weight = 37599.619| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.05 r_work: 0.3611 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19079 Z= 0.187 Angle : 0.815 12.805 25799 Z= 0.411 Chirality : 0.044 0.237 2825 Planarity : 0.005 0.095 3403 Dihedral : 4.818 43.853 2571 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.30 % Allowed : 35.03 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.18), residues: 2293 helix: 1.25 (0.15), residues: 1229 sheet: -1.42 (0.57), residues: 95 loop : -1.95 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 112 TYR 0.048 0.002 TYR O 166 PHE 0.031 0.002 PHE S 333 TRP 0.057 0.002 TRP S 189 HIS 0.007 0.001 HIS R 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (19079) covalent geometry : angle 0.81513 / 0.41 (25799) hydrogen bonds : bond 0.04134 / 2.75 ( 912) hydrogen bonds : angle 4.30789 / 2.99 ( 2673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8663.75 seconds wall clock time: 147 minutes 53.01 seconds (8873.01 seconds total)