Starting phenix.real_space_refine on Sun Aug 24 10:00:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fvu_29493/08_2025/8fvu_29493_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fvu_29493/08_2025/8fvu_29493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fvu_29493/08_2025/8fvu_29493_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fvu_29493/08_2025/8fvu_29493_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fvu_29493/08_2025/8fvu_29493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fvu_29493/08_2025/8fvu_29493.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3 5.49 5 S 112 5.16 5 C 11977 2.51 5 N 3158 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10905 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1304} Chain breaks: 1 Chain: "B" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7198 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "U" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' ZN': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 797 SG CYS A 100 75.533 37.632 96.426 1.00 47.62 S ATOM 989 SG CYS A 124 73.744 36.827 100.409 1.00 38.63 S ATOM 1576 SG CYS A 197 76.104 61.055 126.030 1.00 45.77 S ATOM 1795 SG CYS A 224 74.378 64.195 127.531 1.00 54.44 S ATOM 2528 SG CYS A 315 54.680 27.911 107.917 1.00 62.82 S ATOM 2551 SG CYS A 318 53.186 26.662 104.504 1.00 48.43 S ATOM 2740 SG CYS A 342 57.763 26.984 104.919 1.00 64.78 S Time building chain proxies: 4.89, per 1000 atoms: 0.26 Number of scatterers: 18758 At special positions: 0 Unit cell: (99.54, 156.42, 147.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 112 16.00 P 3 15.00 O 3505 8.00 N 3158 7.00 C 11977 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: 2.02 Conformation dependent library (CDL) restraints added in 974.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 117 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 124 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 100 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A 217 " pdb="ZN ZN A1503 " - pdb=" SG CYS A 224 " pdb="ZN ZN A1503 " - pdb=" SG CYS A 197 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" NE2 HIS A 335 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 318 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 342 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 315 " Number of angles added : 3 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 13 sheets defined 48.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.784A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.770A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 177 through 184 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.738A pdb=" N LYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 395 through 413 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.549A pdb=" N LEU A 434 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 removed outlier: 4.350A pdb=" N PHE A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 460 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 515 through 523 removed outlier: 4.181A pdb=" N ASP A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.562A pdb=" N GLN A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 4.241A pdb=" N LEU A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 618 through 632 removed outlier: 3.854A pdb=" N LYS A 624 " --> pdb=" O THR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.646A pdb=" N GLN A 636 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.850A pdb=" N VAL A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 684 through 700 Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 722 through 726 removed outlier: 3.712A pdb=" N MET A 725 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 764 through 767 Processing helix chain 'A' and resid 768 through 776 removed outlier: 3.760A pdb=" N LEU A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.515A pdb=" N LYS A 806 " --> pdb=" O LYS A 802 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 810 " --> pdb=" O LYS A 806 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.609A pdb=" N GLU A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 851 removed outlier: 3.743A pdb=" N LEU A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 846 " --> pdb=" O GLN A 842 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 874 Processing helix chain 'A' and resid 876 through 879 Processing helix chain 'A' and resid 880 through 889 removed outlier: 3.613A pdb=" N GLN A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'A' and resid 901 through 906 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 956 through 976 removed outlier: 4.249A pdb=" N TYR A 974 " --> pdb=" O ASN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 Processing helix chain 'A' and resid 1039 through 1043 removed outlier: 3.526A pdb=" N GLU A1042 " --> pdb=" O GLY A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1144 through 1153 Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1178 through 1180 No H-bonds generated for 'chain 'A' and resid 1178 through 1180' Processing helix chain 'A' and resid 1195 through 1202 removed outlier: 3.757A pdb=" N SER A1201 " --> pdb=" O PRO A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1220 through 1231 Processing helix chain 'A' and resid 1245 through 1251 Processing helix chain 'A' and resid 1251 through 1258 removed outlier: 4.143A pdb=" N ILE A1255 " --> pdb=" O VAL A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1279 through 1289 removed outlier: 4.308A pdb=" N ALA A1283 " --> pdb=" O VAL A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1315 removed outlier: 3.548A pdb=" N PHE A1313 " --> pdb=" O GLY A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1335 removed outlier: 3.965A pdb=" N CYS A1335 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 removed outlier: 3.768A pdb=" N LEU A1351 " --> pdb=" O SER A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 removed outlier: 3.762A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1381 No H-bonds generated for 'chain 'A' and resid 1379 through 1381' Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 110 through 114 removed outlier: 6.315A pdb=" N SER B 113 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 4.274A pdb=" N GLN B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 238 through 241 removed outlier: 3.832A pdb=" N GLN B 241 " --> pdb=" O LYS B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.573A pdb=" N GLU B 262 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 314 through 328 removed outlier: 4.084A pdb=" N GLN B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 336 through 341 removed outlier: 6.749A pdb=" N LEU B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 382 through 403 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 443 through 460 Processing helix chain 'B' and resid 463 through 476 removed outlier: 3.768A pdb=" N LYS B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 498 through 510 Processing helix chain 'B' and resid 529 through 534 removed outlier: 4.006A pdb=" N LEU B 534 " --> pdb=" O ARG B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.572A pdb=" N ILE B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.583A pdb=" N VAL B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.701A pdb=" N LYS B 682 " --> pdb=" O ARG B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 removed outlier: 4.462A pdb=" N LEU B 708 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER B 709 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 733 Processing helix chain 'B' and resid 779 through 789 removed outlier: 3.794A pdb=" N ASN B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 922 through 931 Processing helix chain 'B' and resid 959 through 964 removed outlier: 3.796A pdb=" N ASN B 963 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 993 Processing helix chain 'B' and resid 1008 through 1015 removed outlier: 3.527A pdb=" N VAL B1014 " --> pdb=" O ASP B1010 " (cutoff:3.500A) Processing helix chain 'U' and resid 1 through 27 removed outlier: 3.546A pdb=" N GLY U 9 " --> pdb=" O ALA U 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP U 12 " --> pdb=" O THR U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 63 removed outlier: 3.855A pdb=" N ILE U 40 " --> pdb=" O ASN U 36 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS U 56 " --> pdb=" O SER U 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 306 Processing sheet with id=AA4, first strand: chain 'A' and resid 450 through 453 removed outlier: 4.442A pdb=" N ILE A 440 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 595 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N CYS A 467 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 546 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU A 578 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE A 548 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA A 580 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU A 550 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ARG A 582 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 500 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 549 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 728 through 731 Processing sheet with id=AA6, first strand: chain 'A' and resid 892 through 894 removed outlier: 6.965A pdb=" N LEU A 893 " --> pdb=" O HIS A 917 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A1030 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A1134 " --> pdb=" O HIS A1161 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS A1163 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A1136 " --> pdb=" O LYS A1163 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A1186 " --> pdb=" O ASN A1212 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A1268 " --> pdb=" O LYS A1298 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A1359 " --> pdb=" O LEU A1390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1336 through 1337 removed outlier: 6.940A pdb=" N ILE A1336 " --> pdb=" O LEU A1365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AA9, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.836A pdb=" N VAL B 149 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 141 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN B 151 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 139 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 294 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB2, first strand: chain 'B' and resid 585 through 587 removed outlier: 6.450A pdb=" N LEU B 662 " --> pdb=" O ARG B 691 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLN B 693 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 664 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LYS B 695 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 666 " --> pdb=" O LYS B 695 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 690 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 716 " --> pdb=" O LEU B 690 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 884 through 885 removed outlier: 7.391A pdb=" N LEU B 884 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 912 " --> pdb=" O ASN B 943 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1000 through 1001 removed outlier: 7.110A pdb=" N ALA B1000 " --> pdb=" O VAL B1022 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 749 hydrogen bonds defined for protein. 2058 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: 5.13 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3687 1.32 - 1.45: 4468 1.45 - 1.57: 10813 1.57 - 1.69: 7 1.69 - 1.82: 163 Bond restraints: 19138 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.19e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.301 0.086 1.00e-02 1.00e+04 7.46e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.490 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C ALA B 295 " pdb=" O ALA B 295 " ideal model delta sigma weight residual 1.236 1.293 -0.058 1.21e-02 6.83e+03 2.29e+01 bond pdb=" C ALA B 295 " pdb=" N GLU B 296 " ideal model delta sigma weight residual 1.330 1.270 0.059 1.39e-02 5.18e+03 1.83e+01 ... (remaining 19133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 25497 3.90 - 7.79: 342 7.79 - 11.69: 13 11.69 - 15.58: 1 15.58 - 19.48: 1 Bond angle restraints: 25854 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 121.45 15.38 1.00e+00 1.00e+00 2.36e+02 angle pdb=" N3 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 127.04 137.23 -10.19 1.15e+00 7.59e-01 7.87e+01 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.22 8.58 1.00e+00 1.00e+00 7.36e+01 angle pdb=" N THR B 360 " pdb=" CA THR B 360 " pdb=" C THR B 360 " ideal model delta sigma weight residual 114.62 104.91 9.71 1.14e+00 7.69e-01 7.26e+01 ... (remaining 25849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11137 17.69 - 35.38: 351 35.38 - 53.06: 72 53.06 - 70.75: 39 70.75 - 88.44: 20 Dihedral angle restraints: 11619 sinusoidal: 4756 harmonic: 6863 Sorted by residual: dihedral pdb=" CA SER A 993 " pdb=" C SER A 993 " pdb=" N PRO A 994 " pdb=" CA PRO A 994 " ideal model delta harmonic sigma weight residual -180.00 -144.12 -35.88 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA SER A 926 " pdb=" C SER A 926 " pdb=" N PRO A 927 " pdb=" CA PRO A 927 " ideal model delta harmonic sigma weight residual 180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A1353 " pdb=" C LEU A1353 " pdb=" N PRO A1354 " pdb=" CA PRO A1354 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 11616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2370 0.086 - 0.173: 511 0.173 - 0.259: 23 0.259 - 0.346: 1 0.346 - 0.432: 1 Chirality restraints: 2906 Sorted by residual: chirality pdb=" CA ALA B 295 " pdb=" N ALA B 295 " pdb=" C ALA B 295 " pdb=" CB ALA B 295 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C1' ATP A1501 " pdb=" C2' ATP A1501 " pdb=" N9 ATP A1501 " pdb=" O4' ATP A1501 " both_signs ideal model delta sigma weight residual False 2.41 2.72 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ILE A 559 " pdb=" N ILE A 559 " pdb=" C ILE A 559 " pdb=" CB ILE A 559 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2903 not shown) Planarity restraints: 3305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1403 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LYS A1403 " -0.058 2.00e-02 2.50e+03 pdb=" O LYS A1403 " 0.021 2.00e-02 2.50e+03 pdb=" OXT LYS A1403 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1310 " -0.030 2.00e-02 2.50e+03 1.61e-02 5.20e+00 pdb=" CG TYR A1310 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A1310 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A1310 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A1310 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A1310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1310 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B1024 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ALA B1024 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA B1024 " 0.013 2.00e-02 2.50e+03 pdb=" OXT ALA B1024 " 0.013 2.00e-02 2.50e+03 ... (remaining 3302 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6455 2.85 - 3.36: 17539 3.36 - 3.88: 30054 3.88 - 4.39: 35980 4.39 - 4.90: 58715 Nonbonded interactions: 148743 Sorted by model distance: nonbonded pdb=" OG1 THR A 189 " pdb=" OG1 THR A 194 " model vdw 2.338 3.040 nonbonded pdb=" OD2 ASP A 828 " pdb=" NZ LYS A1385 " model vdw 2.342 3.120 nonbonded pdb=" OG SER A 796 " pdb=" OG1 THR A 870 " model vdw 2.343 3.040 nonbonded pdb=" OD1 ASP A 552 " pdb=" NZ LYS A 554 " model vdw 2.352 3.120 nonbonded pdb=" NZ LYS A 476 " pdb=" O1G ATP A1501 " model vdw 2.394 3.120 ... (remaining 148738 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 group one per residue 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: 9.850 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 24.060 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.014 0.692 19148 Z= 0.702 Angle : 1.228 19.480 25857 Z= 0.849 Chirality : 0.065 0.432 2906 Planarity : 0.004 0.033 3305 Dihedral : 10.950 88.439 7155 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 1.41 % Allowed : 6.86 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 1.25 % 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 aren not related in a simple way. whole: -1.70 (0.16), residues: 2334 helix: -1.03 (0.14), residues: 1070 sheet: -0.59 (0.31), residues: 264 loop : -1.22 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 497 TYR 0.030 0.004 TYR A1310 PHE 0.018 0.003 PHE A 701 TRP 0.019 0.004 TRP B 917 HIS 0.005 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.01177 (19138) covalent geometry : angle 1.22127 (25854) hydrogen bonds : bond 0.20381 ( 749) hydrogen bonds : angle 7.07713 ( 2058) metal coordination : bond 0.32562 ( 10) metal coordination : angle 11.60712 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4910 (ppp) cc_final: 0.4342 (ppp) REVERT: A 248 ASP cc_start: 0.7646 (t0) cc_final: 0.7439 (t0) REVERT: A 283 ASP cc_start: 0.8324 (t0) cc_final: 0.8092 (m-30) REVERT: A 398 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8552 (tm-30) REVERT: A 583 THR cc_start: 0.8991 (p) cc_final: 0.8540 (t) REVERT: A 672 GLU cc_start: 0.8210 (tp30) cc_final: 0.7847 (tp30) REVERT: A 684 ILE cc_start: 0.8377 (mm) cc_final: 0.8176 (mt) REVERT: A 718 ASP cc_start: 0.8302 (t0) cc_final: 0.7867 (t70) REVERT: A 739 PHE cc_start: 0.8780 (p90) cc_final: 0.8339 (p90) REVERT: A 813 HIS cc_start: 0.8251 (t70) cc_final: 0.8035 (t-90) REVERT: A 946 ILE cc_start: 0.8587 (mp) cc_final: 0.8332 (pt) REVERT: A 1100 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8514 (ttmm) REVERT: A 1154 SER cc_start: 0.7810 (m) cc_final: 0.7350 (p) REVERT: A 1190 ASP cc_start: 0.7696 (t0) cc_final: 0.7356 (t70) REVERT: B 125 ASP cc_start: 0.8267 (t0) cc_final: 0.8054 (t0) REVERT: B 367 TYR cc_start: 0.7756 (t80) cc_final: 0.7374 (t80) REVERT: B 423 THR cc_start: 0.7259 (m) cc_final: 0.6790 (p) REVERT: B 674 LYS cc_start: 0.7732 (tttt) cc_final: 0.7520 (tptt) REVERT: B 970 PHE cc_start: 0.7668 (p90) cc_final: 0.7086 (p90) REVERT: U 12 ASP cc_start: 0.8070 (t70) cc_final: 0.7703 (t0) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1572 time to fit residues: 119.9112 Evaluate side-chains 221 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 545 GLN A 584 ASN A 639 GLN A 862 HIS A 875 ASN A1033 HIS A1036 HIS A1381 HIS B 145 HIS B 180 GLN B 552 ASN B 800 HIS U 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.149843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106327 restraints weight = 30817.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109441 restraints weight = 18173.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111793 restraints weight = 12936.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112180 restraints weight = 10907.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112151 restraints weight = 9888.117| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 19148 Z= 0.163 Angle : 0.711 12.256 25857 Z= 0.374 Chirality : 0.045 0.207 2906 Planarity : 0.004 0.038 3305 Dihedral : 5.924 82.230 2530 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.46 % Favored : 92.33 % Rotamer: Outliers : 2.29 % Allowed : 8.54 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.87 (0.18), residues: 2334 helix: 0.29 (0.16), residues: 1058 sheet: -0.70 (0.32), residues: 267 loop : -1.43 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 332 TYR 0.017 0.002 TYR B 594 PHE 0.026 0.002 PHE A 246 TRP 0.029 0.002 TRP B 186 HIS 0.008 0.001 HIS B 797 Details of bonding type rmsd covalent geometry : bond 0.00367 (19138) covalent geometry : angle 0.70951 (25854) hydrogen bonds : bond 0.05107 ( 749) hydrogen bonds : angle 4.80280 ( 2058) metal coordination : bond 0.01640 ( 10) metal coordination : angle 4.43207 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASP cc_start: 0.6820 (t0) cc_final: 0.6605 (t70) REVERT: A 323 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: A 333 ASP cc_start: 0.8371 (m-30) cc_final: 0.8109 (m-30) REVERT: A 346 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7150 (mm-40) REVERT: A 398 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8171 (tm-30) REVERT: A 552 ASP cc_start: 0.8280 (t0) cc_final: 0.8080 (t70) REVERT: A 783 MET cc_start: 0.8182 (mtp) cc_final: 0.7728 (mmm) REVERT: A 874 SER cc_start: 0.9006 (m) cc_final: 0.8732 (p) REVERT: A 931 PHE cc_start: 0.7702 (m-80) cc_final: 0.7431 (m-80) REVERT: A 1016 MET cc_start: 0.8898 (tpp) cc_final: 0.8695 (tpp) REVERT: A 1176 MET cc_start: 0.7852 (tpp) cc_final: 0.7404 (tpp) REVERT: A 1190 ASP cc_start: 0.7017 (t0) cc_final: 0.6560 (t70) REVERT: A 1363 SER cc_start: 0.9187 (m) cc_final: 0.8974 (p) REVERT: A 1401 ILE cc_start: 0.8123 (mm) cc_final: 0.7674 (mm) REVERT: B 147 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.7048 (t-90) REVERT: B 149 VAL cc_start: 0.6033 (p) cc_final: 0.5710 (m) REVERT: B 235 MET cc_start: 0.8216 (ptp) cc_final: 0.7858 (mtp) REVERT: B 237 LEU cc_start: 0.7536 (mt) cc_final: 0.7277 (mt) REVERT: B 254 LYS cc_start: 0.7348 (ttpp) cc_final: 0.7126 (ttpp) REVERT: B 256 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7439 (mp10) REVERT: B 727 GLU cc_start: 0.7953 (mp0) cc_final: 0.7510 (pp20) REVERT: B 775 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6221 (ttt) REVERT: B 875 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6441 (ptp) REVERT: B 958 MET cc_start: 0.6782 (mmm) cc_final: 0.6571 (mmm) REVERT: U 12 ASP cc_start: 0.8200 (t70) cc_final: 0.7738 (t0) REVERT: U 36 ASN cc_start: 0.8734 (m-40) cc_final: 0.8370 (m110) REVERT: U 40 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7877 (mp) outliers start: 48 outliers final: 26 residues processed: 309 average time/residue: 0.1326 time to fit residues: 63.9402 Evaluate side-chains 223 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 40 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 149 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 223 optimal weight: 0.0570 chunk 136 optimal weight: 8.9990 chunk 12 optimal weight: 0.0060 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 225 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110741 restraints weight = 30830.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111012 restraints weight = 22014.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112010 restraints weight = 17331.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112677 restraints weight = 13779.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112933 restraints weight = 12690.280| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 19148 Z= 0.116 Angle : 0.607 14.766 25857 Z= 0.318 Chirality : 0.042 0.228 2906 Planarity : 0.004 0.037 3305 Dihedral : 5.544 78.372 2530 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.05 % Favored : 91.82 % Rotamer: Outliers : 2.05 % Allowed : 9.83 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.57 (0.18), residues: 2334 helix: 0.74 (0.17), residues: 1056 sheet: -0.62 (0.33), residues: 257 loop : -1.50 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.018 0.001 TYR B 594 PHE 0.020 0.001 PHE A 750 TRP 0.042 0.002 TRP B 186 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00246 (19138) covalent geometry : angle 0.60578 (25854) hydrogen bonds : bond 0.04058 ( 749) hydrogen bonds : angle 4.26311 ( 2058) metal coordination : bond 0.00744 ( 10) metal coordination : angle 3.22235 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4470 (ppp) cc_final: 0.4106 (ppp) REVERT: A 313 VAL cc_start: 0.8945 (t) cc_final: 0.8726 (p) REVERT: A 333 ASP cc_start: 0.8368 (m-30) cc_final: 0.8159 (m-30) REVERT: A 346 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7076 (mm-40) REVERT: A 398 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8136 (tm-30) REVERT: A 496 ASN cc_start: 0.8283 (p0) cc_final: 0.7956 (p0) REVERT: A 552 ASP cc_start: 0.8295 (t0) cc_final: 0.8071 (t70) REVERT: A 626 MET cc_start: 0.8434 (mmm) cc_final: 0.8146 (mmm) REVERT: A 874 SER cc_start: 0.8855 (m) cc_final: 0.8550 (p) REVERT: A 931 PHE cc_start: 0.7715 (m-80) cc_final: 0.7247 (m-80) REVERT: A 1106 GLU cc_start: 0.7302 (tt0) cc_final: 0.7073 (mt-10) REVERT: A 1174 MET cc_start: 0.8486 (mmm) cc_final: 0.7979 (mpp) REVERT: A 1176 MET cc_start: 0.7960 (tpp) cc_final: 0.7503 (tpp) REVERT: A 1241 ILE cc_start: 0.8831 (mm) cc_final: 0.8582 (mm) REVERT: A 1363 SER cc_start: 0.9193 (m) cc_final: 0.8967 (p) REVERT: B 203 LEU cc_start: 0.8382 (mp) cc_final: 0.8150 (mm) REVERT: B 235 MET cc_start: 0.7941 (ptp) cc_final: 0.7395 (mtp) REVERT: B 237 LEU cc_start: 0.7666 (mt) cc_final: 0.7456 (mt) REVERT: B 248 ASP cc_start: 0.7200 (p0) cc_final: 0.6972 (p0) REVERT: B 256 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7468 (mp10) REVERT: B 300 MET cc_start: 0.6613 (ttm) cc_final: 0.6305 (tmm) REVERT: B 408 PHE cc_start: 0.6944 (m-10) cc_final: 0.6717 (m-80) REVERT: B 727 GLU cc_start: 0.7904 (mp0) cc_final: 0.7450 (tm-30) REVERT: B 775 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5915 (ttt) REVERT: B 927 LEU cc_start: 0.8912 (mt) cc_final: 0.8711 (tp) REVERT: B 958 MET cc_start: 0.6469 (mmm) cc_final: 0.6244 (mmm) REVERT: U 12 ASP cc_start: 0.8123 (t70) cc_final: 0.7681 (t0) REVERT: U 15 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7764 (tp-100) REVERT: U 56 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8550 (ttmt) outliers start: 43 outliers final: 25 residues processed: 264 average time/residue: 0.1239 time to fit residues: 53.3251 Evaluate side-chains 208 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 32 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 633 GLN B 147 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109063 restraints weight = 31029.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109689 restraints weight = 21026.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110282 restraints weight = 18563.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110954 restraints weight = 15548.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111265 restraints weight = 13962.737| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19148 Z= 0.137 Angle : 0.604 14.882 25857 Z= 0.316 Chirality : 0.043 0.184 2906 Planarity : 0.004 0.038 3305 Dihedral : 5.593 86.026 2530 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 2.62 % Allowed : 10.54 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.59 (0.18), residues: 2334 helix: 0.82 (0.17), residues: 1057 sheet: -0.80 (0.33), residues: 256 loop : -1.59 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 228 TYR 0.016 0.001 TYR A 605 PHE 0.016 0.001 PHE A 750 TRP 0.048 0.002 TRP B 186 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00314 (19138) covalent geometry : angle 0.60329 (25854) hydrogen bonds : bond 0.03954 ( 749) hydrogen bonds : angle 4.18943 ( 2058) metal coordination : bond 0.01005 ( 10) metal coordination : angle 2.73341 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4716 (ppp) cc_final: 0.4243 (ppp) REVERT: A 211 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: A 305 PHE cc_start: 0.8526 (p90) cc_final: 0.8242 (p90) REVERT: A 313 VAL cc_start: 0.9044 (t) cc_final: 0.8831 (p) REVERT: A 346 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7222 (mm-40) REVERT: A 398 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8112 (tm-30) REVERT: A 496 ASN cc_start: 0.8292 (p0) cc_final: 0.7999 (p0) REVERT: A 552 ASP cc_start: 0.8326 (t0) cc_final: 0.8077 (t70) REVERT: A 985 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8074 (pp) REVERT: A 1176 MET cc_start: 0.8037 (tpp) cc_final: 0.7538 (tpp) REVERT: A 1190 ASP cc_start: 0.6551 (t0) cc_final: 0.6046 (t70) REVERT: A 1241 ILE cc_start: 0.8957 (mm) cc_final: 0.8687 (mm) REVERT: B 123 ASP cc_start: 0.7751 (m-30) cc_final: 0.7447 (p0) REVERT: B 235 MET cc_start: 0.7764 (ptp) cc_final: 0.7194 (mtp) REVERT: B 247 LEU cc_start: 0.7600 (mm) cc_final: 0.7145 (tp) REVERT: U 12 ASP cc_start: 0.8192 (t70) cc_final: 0.7771 (t0) REVERT: U 15 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7807 (tp-100) REVERT: U 40 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7812 (mp) outliers start: 55 outliers final: 39 residues processed: 239 average time/residue: 0.1209 time to fit residues: 47.5459 Evaluate side-chains 218 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 26 LYS Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 108 optimal weight: 0.0060 chunk 46 optimal weight: 0.2980 chunk 156 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 463 ASN A 606 ASN B 147 HIS B 151 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS B 902 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108877 restraints weight = 31002.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106457 restraints weight = 25546.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108078 restraints weight = 21525.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109150 restraints weight = 15779.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109294 restraints weight = 14189.721| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19148 Z= 0.141 Angle : 0.596 14.249 25857 Z= 0.310 Chirality : 0.043 0.236 2906 Planarity : 0.003 0.034 3305 Dihedral : 5.667 88.511 2530 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.93 % Favored : 91.95 % Rotamer: Outliers : 2.34 % Allowed : 10.93 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.58 (0.18), residues: 2334 helix: 0.90 (0.17), residues: 1056 sheet: -0.92 (0.32), residues: 270 loop : -1.64 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1330 TYR 0.018 0.001 TYR A 605 PHE 0.016 0.001 PHE A 226 TRP 0.066 0.002 TRP B 186 HIS 0.009 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00329 (19138) covalent geometry : angle 0.59565 (25854) hydrogen bonds : bond 0.03897 ( 749) hydrogen bonds : angle 4.14484 ( 2058) metal coordination : bond 0.00959 ( 10) metal coordination : angle 2.20675 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4464 (ppp) cc_final: 0.4241 (ppp) REVERT: A 313 VAL cc_start: 0.9081 (t) cc_final: 0.8825 (p) REVERT: A 346 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7360 (mm-40) REVERT: A 463 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.6853 (t0) REVERT: A 496 ASN cc_start: 0.8411 (p0) cc_final: 0.8103 (p0) REVERT: A 552 ASP cc_start: 0.8346 (t0) cc_final: 0.8093 (t70) REVERT: A 985 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8194 (pp) REVERT: A 1131 MET cc_start: 0.7821 (tpp) cc_final: 0.7374 (mpp) REVERT: A 1176 MET cc_start: 0.8002 (tpp) cc_final: 0.7438 (tpp) REVERT: A 1190 ASP cc_start: 0.6553 (t0) cc_final: 0.6118 (t70) REVERT: A 1241 ILE cc_start: 0.8960 (mm) cc_final: 0.8673 (mm) REVERT: B 123 ASP cc_start: 0.7781 (m-30) cc_final: 0.7422 (p0) REVERT: B 235 MET cc_start: 0.7847 (ptp) cc_final: 0.7266 (mtp) REVERT: B 247 LEU cc_start: 0.7765 (mm) cc_final: 0.7277 (tp) REVERT: B 727 GLU cc_start: 0.7931 (mp0) cc_final: 0.7510 (tm-30) REVERT: B 958 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6530 (mmm) REVERT: U 12 ASP cc_start: 0.8220 (t70) cc_final: 0.7816 (t0) REVERT: U 44 TYR cc_start: 0.8648 (t80) cc_final: 0.8284 (t80) REVERT: U 56 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8443 (ttmt) outliers start: 49 outliers final: 33 residues processed: 220 average time/residue: 0.1228 time to fit residues: 44.8109 Evaluate side-chains 209 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN A 651 HIS A 930 HIS B 147 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104584 restraints weight = 30771.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105461 restraints weight = 22774.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105652 restraints weight = 19296.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107576 restraints weight = 16218.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107444 restraints weight = 13518.738| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19148 Z= 0.188 Angle : 0.633 13.981 25857 Z= 0.328 Chirality : 0.045 0.333 2906 Planarity : 0.004 0.035 3305 Dihedral : 5.876 88.723 2530 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 2.48 % Allowed : 11.45 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.75 (0.18), residues: 2334 helix: 0.86 (0.17), residues: 1053 sheet: -1.25 (0.33), residues: 253 loop : -1.75 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1330 TYR 0.021 0.002 TYR A 605 PHE 0.029 0.002 PHE A 226 TRP 0.076 0.002 TRP B 186 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00452 (19138) covalent geometry : angle 0.63292 (25854) hydrogen bonds : bond 0.04337 ( 749) hydrogen bonds : angle 4.25928 ( 2058) metal coordination : bond 0.01309 ( 10) metal coordination : angle 2.00564 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 VAL cc_start: 0.9201 (t) cc_final: 0.8987 (p) REVERT: A 346 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 552 ASP cc_start: 0.8347 (t0) cc_final: 0.8124 (t70) REVERT: A 841 MET cc_start: 0.8746 (mmm) cc_final: 0.8342 (mmm) REVERT: A 985 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8087 (pp) REVERT: A 1131 MET cc_start: 0.7849 (tpp) cc_final: 0.7420 (mpp) REVERT: A 1176 MET cc_start: 0.8052 (tpp) cc_final: 0.7531 (tpp) REVERT: A 1190 ASP cc_start: 0.6657 (t0) cc_final: 0.6230 (t70) REVERT: A 1241 ILE cc_start: 0.9056 (mm) cc_final: 0.8775 (mm) REVERT: B 123 ASP cc_start: 0.7782 (m-30) cc_final: 0.7420 (p0) REVERT: B 235 MET cc_start: 0.7656 (ptp) cc_final: 0.7049 (mtp) REVERT: B 597 ASP cc_start: 0.8249 (m-30) cc_final: 0.7992 (m-30) REVERT: B 727 GLU cc_start: 0.7840 (mp0) cc_final: 0.7507 (tm-30) REVERT: U 12 ASP cc_start: 0.8294 (t70) cc_final: 0.7904 (t0) REVERT: U 15 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8037 (tp-100) REVERT: U 40 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7934 (mp) REVERT: U 44 TYR cc_start: 0.8704 (t80) cc_final: 0.8412 (t80) outliers start: 52 outliers final: 34 residues processed: 222 average time/residue: 0.1223 time to fit residues: 44.7617 Evaluate side-chains 206 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 930 HIS B 147 HIS B 159 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105035 restraints weight = 31013.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105680 restraints weight = 22419.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105899 restraints weight = 19464.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108578 restraints weight = 16316.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108334 restraints weight = 12870.077| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19148 Z= 0.158 Angle : 0.605 13.813 25857 Z= 0.313 Chirality : 0.044 0.208 2906 Planarity : 0.004 0.035 3305 Dihedral : 5.872 84.983 2530 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.70 % Favored : 91.17 % Rotamer: Outliers : 2.34 % Allowed : 11.74 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.70 (0.18), residues: 2334 helix: 0.90 (0.17), residues: 1052 sheet: -1.32 (0.34), residues: 251 loop : -1.70 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 585 TYR 0.018 0.001 TYR A 605 PHE 0.022 0.001 PHE A 226 TRP 0.056 0.002 TRP B 186 HIS 0.020 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00375 (19138) covalent geometry : angle 0.60484 (25854) hydrogen bonds : bond 0.04032 ( 749) hydrogen bonds : angle 4.16955 ( 2058) metal coordination : bond 0.01071 ( 10) metal coordination : angle 1.96914 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 VAL cc_start: 0.9207 (t) cc_final: 0.8997 (p) REVERT: A 333 ASP cc_start: 0.8370 (m-30) cc_final: 0.8082 (m-30) REVERT: A 346 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7478 (mm-40) REVERT: A 552 ASP cc_start: 0.8347 (t0) cc_final: 0.8097 (t70) REVERT: A 584 ASN cc_start: 0.8811 (m-40) cc_final: 0.8592 (m-40) REVERT: A 672 GLU cc_start: 0.8021 (tp30) cc_final: 0.7810 (tp30) REVERT: A 985 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8073 (pp) REVERT: A 1131 MET cc_start: 0.7906 (tpp) cc_final: 0.7514 (mpp) REVERT: A 1176 MET cc_start: 0.8090 (tpp) cc_final: 0.7541 (tpp) REVERT: A 1190 ASP cc_start: 0.6675 (t0) cc_final: 0.6299 (t0) REVERT: A 1241 ILE cc_start: 0.9032 (mm) cc_final: 0.8753 (mm) REVERT: B 235 MET cc_start: 0.7620 (ptp) cc_final: 0.6981 (mtp) REVERT: B 597 ASP cc_start: 0.8237 (m-30) cc_final: 0.7993 (m-30) REVERT: B 727 GLU cc_start: 0.7753 (mp0) cc_final: 0.7488 (tm-30) REVERT: U 12 ASP cc_start: 0.8258 (t70) cc_final: 0.7907 (t0) REVERT: U 15 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8002 (tp-100) REVERT: U 40 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7880 (mp) REVERT: U 44 TYR cc_start: 0.8677 (t80) cc_final: 0.8273 (t80) REVERT: U 56 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8432 (ttmt) outliers start: 49 outliers final: 36 residues processed: 212 average time/residue: 0.1242 time to fit residues: 43.3147 Evaluate side-chains 207 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 43 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 133 optimal weight: 0.0270 chunk 195 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 199 optimal weight: 0.0470 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 633 GLN B 147 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106840 restraints weight = 30982.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106576 restraints weight = 22095.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107795 restraints weight = 18913.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108113 restraints weight = 15170.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108380 restraints weight = 13691.666| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19148 Z= 0.119 Angle : 0.570 13.536 25857 Z= 0.295 Chirality : 0.042 0.196 2906 Planarity : 0.003 0.033 3305 Dihedral : 5.737 88.380 2530 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.35 % Favored : 91.47 % Rotamer: Outliers : 2.10 % Allowed : 12.12 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.58 (0.18), residues: 2334 helix: 1.05 (0.17), residues: 1043 sheet: -1.26 (0.34), residues: 252 loop : -1.67 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.014 0.001 TYR B 594 PHE 0.021 0.001 PHE A 226 TRP 0.049 0.002 TRP B 186 HIS 0.011 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00271 (19138) covalent geometry : angle 0.56955 (25854) hydrogen bonds : bond 0.03541 ( 749) hydrogen bonds : angle 4.01158 ( 2058) metal coordination : bond 0.00897 ( 10) metal coordination : angle 2.03012 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3756 (ppp) cc_final: 0.3443 (ppp) REVERT: A 313 VAL cc_start: 0.9164 (t) cc_final: 0.8959 (p) REVERT: A 333 ASP cc_start: 0.8377 (m-30) cc_final: 0.8073 (m-30) REVERT: A 552 ASP cc_start: 0.8337 (t0) cc_final: 0.8069 (t70) REVERT: A 584 ASN cc_start: 0.8817 (m-40) cc_final: 0.8554 (m-40) REVERT: A 782 MET cc_start: 0.9032 (tpp) cc_final: 0.8645 (ttm) REVERT: A 985 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 1131 MET cc_start: 0.7942 (tpp) cc_final: 0.7522 (mpp) REVERT: A 1170 PHE cc_start: 0.7689 (t80) cc_final: 0.7298 (t80) REVERT: A 1176 MET cc_start: 0.8110 (tpp) cc_final: 0.7635 (tpp) REVERT: A 1190 ASP cc_start: 0.6571 (t0) cc_final: 0.6196 (t70) REVERT: A 1241 ILE cc_start: 0.8945 (mm) cc_final: 0.8648 (mm) REVERT: B 235 MET cc_start: 0.7699 (ptp) cc_final: 0.7088 (tmm) REVERT: B 597 ASP cc_start: 0.8219 (m-30) cc_final: 0.7937 (m-30) REVERT: B 727 GLU cc_start: 0.7891 (mp0) cc_final: 0.7536 (tm-30) REVERT: U 12 ASP cc_start: 0.8235 (t70) cc_final: 0.7863 (t0) REVERT: U 40 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7871 (mp) REVERT: U 44 TYR cc_start: 0.8637 (t80) cc_final: 0.8259 (t80) REVERT: U 56 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8399 (ttmt) outliers start: 44 outliers final: 34 residues processed: 216 average time/residue: 0.1231 time to fit residues: 43.7251 Evaluate side-chains 201 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 109 optimal weight: 0.0000 chunk 44 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 41 optimal weight: 0.0000 chunk 76 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 633 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN U 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.147452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107369 restraints weight = 30638.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106950 restraints weight = 23106.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108532 restraints weight = 19260.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108834 restraints weight = 15344.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109100 restraints weight = 13688.525| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19148 Z= 0.107 Angle : 0.577 16.848 25857 Z= 0.297 Chirality : 0.042 0.188 2906 Planarity : 0.003 0.034 3305 Dihedral : 5.647 88.174 2530 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.23 % Favored : 91.60 % Rotamer: Outliers : 1.81 % Allowed : 12.93 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.49 (0.19), residues: 2334 helix: 1.15 (0.17), residues: 1038 sheet: -1.17 (0.34), residues: 257 loop : -1.66 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.014 0.001 TYR B 594 PHE 0.020 0.001 PHE A 226 TRP 0.042 0.002 TRP B 186 HIS 0.019 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00233 (19138) covalent geometry : angle 0.57689 (25854) hydrogen bonds : bond 0.03345 ( 749) hydrogen bonds : angle 3.97738 ( 2058) metal coordination : bond 0.00654 ( 10) metal coordination : angle 1.83859 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3780 (ppp) cc_final: 0.3441 (ppp) REVERT: A 333 ASP cc_start: 0.8380 (m-30) cc_final: 0.8084 (m-30) REVERT: A 346 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7418 (mm-40) REVERT: A 496 ASN cc_start: 0.8383 (p0) cc_final: 0.8159 (p0) REVERT: A 552 ASP cc_start: 0.8324 (t0) cc_final: 0.8051 (t70) REVERT: A 584 ASN cc_start: 0.8753 (m-40) cc_final: 0.8519 (m-40) REVERT: A 782 MET cc_start: 0.9048 (tpp) cc_final: 0.8664 (ttm) REVERT: A 985 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8088 (pp) REVERT: A 1131 MET cc_start: 0.7898 (tpp) cc_final: 0.7455 (mpp) REVERT: A 1170 PHE cc_start: 0.7736 (t80) cc_final: 0.7317 (t80) REVERT: A 1176 MET cc_start: 0.8115 (tpp) cc_final: 0.7607 (tpp) REVERT: A 1190 ASP cc_start: 0.6598 (t0) cc_final: 0.6216 (t0) REVERT: B 235 MET cc_start: 0.7656 (ptp) cc_final: 0.6819 (tmm) REVERT: B 597 ASP cc_start: 0.8178 (m-30) cc_final: 0.7887 (m-30) REVERT: B 727 GLU cc_start: 0.7894 (mp0) cc_final: 0.7584 (pp20) REVERT: B 875 MET cc_start: 0.6538 (pmm) cc_final: 0.5924 (pmm) REVERT: B 917 TRP cc_start: 0.5779 (p-90) cc_final: 0.3784 (p-90) REVERT: B 942 LEU cc_start: 0.7365 (tp) cc_final: 0.7139 (tp) REVERT: B 958 MET cc_start: 0.6662 (mmp) cc_final: 0.6436 (mmp) REVERT: U 12 ASP cc_start: 0.8246 (t70) cc_final: 0.7862 (t0) REVERT: U 40 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7842 (mp) REVERT: U 44 TYR cc_start: 0.8616 (t80) cc_final: 0.8272 (t80) outliers start: 38 outliers final: 32 residues processed: 210 average time/residue: 0.1267 time to fit residues: 43.4976 Evaluate side-chains 205 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 134 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 96 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 chunk 88 optimal weight: 0.0870 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106629 restraints weight = 30706.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108057 restraints weight = 21558.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109232 restraints weight = 15545.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109625 restraints weight = 13372.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109900 restraints weight = 12710.981| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19148 Z= 0.113 Angle : 0.575 16.774 25857 Z= 0.296 Chirality : 0.042 0.183 2906 Planarity : 0.003 0.033 3305 Dihedral : 5.566 86.441 2530 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.99 % Rotamer: Outliers : 1.72 % Allowed : 12.88 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.43 (0.19), residues: 2334 helix: 1.20 (0.17), residues: 1041 sheet: -1.18 (0.34), residues: 258 loop : -1.62 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.014 0.001 TYR B 594 PHE 0.019 0.001 PHE A 226 TRP 0.060 0.002 TRP B 186 HIS 0.011 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00253 (19138) covalent geometry : angle 0.57475 (25854) hydrogen bonds : bond 0.03311 ( 749) hydrogen bonds : angle 3.96719 ( 2058) metal coordination : bond 0.00809 ( 10) metal coordination : angle 1.74875 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3583 (ppp) cc_final: 0.3253 (ppp) REVERT: A 332 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 333 ASP cc_start: 0.8372 (m-30) cc_final: 0.8062 (m-30) REVERT: A 346 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7388 (mm-40) REVERT: A 552 ASP cc_start: 0.8308 (t0) cc_final: 0.8017 (t70) REVERT: A 584 ASN cc_start: 0.8738 (m-40) cc_final: 0.8486 (m-40) REVERT: A 606 ASN cc_start: 0.8305 (m110) cc_final: 0.8001 (m110) REVERT: A 782 MET cc_start: 0.8998 (tpp) cc_final: 0.8723 (ttm) REVERT: A 783 MET cc_start: 0.8460 (mtp) cc_final: 0.8248 (mmm) REVERT: A 985 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8161 (pp) REVERT: A 1131 MET cc_start: 0.7890 (tpp) cc_final: 0.7456 (mpp) REVERT: A 1176 MET cc_start: 0.8080 (tpp) cc_final: 0.7691 (tpp) REVERT: A 1190 ASP cc_start: 0.6588 (t0) cc_final: 0.6257 (t0) REVERT: B 235 MET cc_start: 0.7595 (ptp) cc_final: 0.7098 (mtp) REVERT: B 597 ASP cc_start: 0.8167 (m-30) cc_final: 0.7870 (m-30) REVERT: B 727 GLU cc_start: 0.7861 (mp0) cc_final: 0.7584 (pp20) REVERT: B 875 MET cc_start: 0.6380 (pmm) cc_final: 0.5855 (pmm) REVERT: B 917 TRP cc_start: 0.5925 (p-90) cc_final: 0.3809 (p-90) REVERT: B 942 LEU cc_start: 0.7291 (tp) cc_final: 0.7066 (tp) REVERT: U 12 ASP cc_start: 0.8226 (t70) cc_final: 0.7861 (t0) REVERT: U 40 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7806 (mp) REVERT: U 44 TYR cc_start: 0.8622 (t80) cc_final: 0.8280 (t80) outliers start: 36 outliers final: 27 residues processed: 205 average time/residue: 0.1231 time to fit residues: 41.4418 Evaluate side-chains 194 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 61 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 306 GLN B 552 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106399 restraints weight = 31050.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106019 restraints weight = 21456.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107185 restraints weight = 16764.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107743 restraints weight = 13943.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108177 restraints weight = 13018.729| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19148 Z= 0.131 Angle : 0.593 16.815 25857 Z= 0.306 Chirality : 0.043 0.185 2906 Planarity : 0.004 0.034 3305 Dihedral : 5.634 89.422 2530 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.57 % Favored : 91.30 % Rotamer: Outliers : 1.72 % Allowed : 13.12 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 aren not related in a simple way. whole: -0.41 (0.19), residues: 2334 helix: 1.23 (0.17), residues: 1041 sheet: -1.19 (0.34), residues: 258 loop : -1.62 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 148 TYR 0.025 0.001 TYR B 859 PHE 0.034 0.001 PHE B 684 TRP 0.062 0.002 TRP B 888 HIS 0.012 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00304 (19138) covalent geometry : angle 0.59321 (25854) hydrogen bonds : bond 0.03481 ( 749) hydrogen bonds : angle 3.99927 ( 2058) metal coordination : bond 0.00801 ( 10) metal coordination : angle 1.39927 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.34 seconds wall clock time: 51 minutes 17.88 seconds (3077.88 seconds total)