Starting phenix.real_space_refine on Mon Jun 16 18:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fvu_29493/06_2025/8fvu_29493_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fvu_29493/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fvu_29493/06_2025/8fvu_29493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fvu_29493/06_2025/8fvu_29493.map" model { file = "/net/cci-nas-00/data/ceres_data/8fvu_29493/06_2025/8fvu_29493_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fvu_29493/06_2025/8fvu_29493_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.89, per 1000 atoms: 0.63 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: 4.89 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.48 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: 9.38 Time building geometry restraints manager: 5.83 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: 3.390 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 52.800 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (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 TRP 0.019 0.004 TRP B 917 HIS 0.005 0.001 HIS B 731 PHE 0.018 0.003 PHE A 701 TYR 0.030 0.004 TYR A1310 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.20381 ( 749) hydrogen bonds : angle 7.07713 ( 2058) metal coordination : bond 0.32562 ( 10) metal coordination : angle 11.60712 ( 3) covalent geometry : bond 0.01177 (19138) covalent geometry : angle 1.22127 (25854) *********************** 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 : 2.507 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: 0.3537 time to fit residues: 269.5907 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 : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 135 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS U 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110584 restraints weight = 30925.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111121 restraints weight = 21379.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112229 restraints weight = 16054.261| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19148 Z= 0.153 Angle : 0.698 12.272 25857 Z= 0.371 Chirality : 0.044 0.239 2906 Planarity : 0.004 0.041 3305 Dihedral : 5.799 80.864 2530 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 2.15 % Allowed : 8.54 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2334 helix: 0.31 (0.16), residues: 1061 sheet: -0.68 (0.32), residues: 269 loop : -1.39 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 186 HIS 0.007 0.001 HIS B 797 PHE 0.023 0.002 PHE A 246 TYR 0.017 0.002 TYR B 594 ARG 0.006 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.05412 ( 749) hydrogen bonds : angle 4.84502 ( 2058) metal coordination : bond 0.01668 ( 10) metal coordination : angle 4.29021 ( 3) covalent geometry : bond 0.00334 (19138) covalent geometry : angle 0.69617 (25854) *********************** 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 321 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4385 (ppp) cc_final: 0.3600 (ppp) REVERT: A 323 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6433 (mm-30) REVERT: A 333 ASP cc_start: 0.8298 (m-30) cc_final: 0.8060 (m-30) REVERT: A 398 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8196 (tm-30) REVERT: A 874 SER cc_start: 0.9020 (m) cc_final: 0.8765 (p) REVERT: A 931 PHE cc_start: 0.7730 (m-80) cc_final: 0.7391 (m-80) REVERT: A 1176 MET cc_start: 0.7922 (tpp) cc_final: 0.7458 (tpp) REVERT: A 1190 ASP cc_start: 0.7031 (t0) cc_final: 0.6468 (t70) REVERT: A 1363 SER cc_start: 0.9234 (m) cc_final: 0.8986 (p) REVERT: A 1370 ASP cc_start: 0.8189 (m-30) cc_final: 0.7980 (m-30) REVERT: A 1401 ILE cc_start: 0.8102 (mm) cc_final: 0.7627 (mm) REVERT: B 125 ASP cc_start: 0.8369 (t0) cc_final: 0.7967 (t0) REVERT: B 235 MET cc_start: 0.7961 (ptp) cc_final: 0.7466 (mtp) REVERT: B 237 LEU cc_start: 0.7377 (mt) cc_final: 0.7121 (mt) REVERT: B 727 GLU cc_start: 0.7919 (mp0) cc_final: 0.7526 (pp20) REVERT: B 775 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6351 (ttt) REVERT: B 847 LEU cc_start: 0.7557 (tp) cc_final: 0.7030 (mp) REVERT: U 12 ASP cc_start: 0.8130 (t70) cc_final: 0.7674 (t0) REVERT: U 36 ASN cc_start: 0.8713 (m-40) cc_final: 0.8360 (m110) REVERT: U 40 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7906 (mp) outliers start: 45 outliers final: 25 residues processed: 310 average time/residue: 0.3062 time to fit residues: 147.5362 Evaluate side-chains 221 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 720 ASP 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 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 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 154 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN B 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105648 restraints weight = 30732.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106413 restraints weight = 21402.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106949 restraints weight = 19105.747| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19148 Z= 0.198 Angle : 0.681 12.540 25857 Z= 0.358 Chirality : 0.046 0.191 2906 Planarity : 0.004 0.041 3305 Dihedral : 5.946 89.275 2530 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.35 % Favored : 91.47 % Rotamer: Outliers : 2.10 % Allowed : 9.92 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2334 helix: 0.52 (0.17), residues: 1060 sheet: -0.77 (0.33), residues: 255 loop : -1.64 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 186 HIS 0.009 0.001 HIS A 121 PHE 0.024 0.002 PHE U 69 TYR 0.021 0.002 TYR A 605 ARG 0.007 0.001 ARG A1330 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 749) hydrogen bonds : angle 4.57568 ( 2058) metal coordination : bond 0.01436 ( 10) metal coordination : angle 3.21763 ( 3) covalent geometry : bond 0.00472 (19138) covalent geometry : angle 0.68055 (25854) *********************** 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 260 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4539 (ppp) cc_final: 0.4096 (ppp) REVERT: A 313 VAL cc_start: 0.9096 (t) cc_final: 0.8873 (p) REVERT: A 333 ASP cc_start: 0.8307 (m-30) cc_final: 0.8064 (m-30) REVERT: A 346 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7374 (mm-40) REVERT: A 398 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8048 (tm-30) REVERT: A 463 ASN cc_start: 0.7532 (t0) cc_final: 0.6833 (t0) REVERT: A 655 TYR cc_start: 0.8318 (m-80) cc_final: 0.8075 (m-10) REVERT: A 822 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 874 SER cc_start: 0.8922 (m) cc_final: 0.8657 (p) REVERT: A 1190 ASP cc_start: 0.6977 (t0) cc_final: 0.6494 (t70) REVERT: A 1241 ILE cc_start: 0.9006 (mm) cc_final: 0.8751 (mm) REVERT: B 203 LEU cc_start: 0.8483 (mp) cc_final: 0.8254 (mm) REVERT: B 235 MET cc_start: 0.7663 (ptp) cc_final: 0.7043 (mtp) REVERT: B 237 LEU cc_start: 0.7505 (mt) cc_final: 0.7290 (mt) REVERT: B 248 ASP cc_start: 0.7187 (p0) cc_final: 0.6984 (p0) REVERT: B 775 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5780 (ttt) REVERT: B 927 LEU cc_start: 0.8690 (mt) cc_final: 0.8479 (tp) REVERT: U 12 ASP cc_start: 0.8234 (t70) cc_final: 0.7860 (t0) REVERT: U 15 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7912 (tp-100) REVERT: U 40 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7912 (mp) outliers start: 44 outliers final: 28 residues processed: 250 average time/residue: 0.2883 time to fit residues: 114.8280 Evaluate side-chains 203 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 323 GLU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 557 CYS 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 915 SER 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 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 339 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 21 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 123 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 253 HIS A 651 HIS ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 357 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.143387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102622 restraints weight = 31232.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102790 restraints weight = 19104.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103004 restraints weight = 16566.320| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19148 Z= 0.250 Angle : 0.704 13.005 25857 Z= 0.369 Chirality : 0.047 0.175 2906 Planarity : 0.004 0.059 3305 Dihedral : 6.367 89.362 2530 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.65 % Favored : 91.13 % Rotamer: Outliers : 2.96 % Allowed : 10.73 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2334 helix: 0.41 (0.17), residues: 1069 sheet: -1.34 (0.31), residues: 270 loop : -1.89 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 186 HIS 0.007 0.001 HIS A 121 PHE 0.023 0.002 PHE U 69 TYR 0.026 0.002 TYR U 37 ARG 0.008 0.001 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 749) hydrogen bonds : angle 4.67041 ( 2058) metal coordination : bond 0.01737 ( 10) metal coordination : angle 2.54201 ( 3) covalent geometry : bond 0.00609 (19138) covalent geometry : angle 0.70337 (25854) *********************** 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 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4479 (ppp) cc_final: 0.4189 (ppp) REVERT: A 248 ASP cc_start: 0.6991 (t0) cc_final: 0.6664 (t0) REVERT: A 313 VAL cc_start: 0.9156 (t) cc_final: 0.8885 (p) REVERT: A 323 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: A 655 TYR cc_start: 0.8405 (m-80) cc_final: 0.8133 (m-10) REVERT: A 822 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 985 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8113 (pp) REVERT: A 1131 MET cc_start: 0.8076 (tpp) cc_final: 0.7568 (mpp) REVERT: A 1176 MET cc_start: 0.8107 (tpp) cc_final: 0.7382 (tpp) REVERT: A 1241 ILE cc_start: 0.9238 (mm) cc_final: 0.8965 (mm) REVERT: B 235 MET cc_start: 0.8011 (ptp) cc_final: 0.7501 (mtp) REVERT: B 247 LEU cc_start: 0.7753 (mm) cc_final: 0.7322 (tp) REVERT: B 597 ASP cc_start: 0.8351 (m-30) cc_final: 0.8136 (m-30) REVERT: B 727 GLU cc_start: 0.8010 (mp0) cc_final: 0.7513 (tm-30) REVERT: B 912 LEU cc_start: 0.8296 (tp) cc_final: 0.7896 (mt) REVERT: B 942 LEU cc_start: 0.7795 (tt) cc_final: 0.7239 (tp) REVERT: B 958 MET cc_start: 0.6850 (mmm) cc_final: 0.6589 (mmm) REVERT: U 12 ASP cc_start: 0.8350 (t70) cc_final: 0.8030 (t0) REVERT: U 15 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7847 (tp-100) REVERT: U 40 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7975 (mp) outliers start: 62 outliers final: 38 residues processed: 241 average time/residue: 0.2868 time to fit residues: 109.1651 Evaluate side-chains 209 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 240 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 323 GLU 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 557 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 584 ASN 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 943 VAL 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 184 MET 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 517 CYS Chi-restraints excluded: chain B residue 895 SER 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 Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 168 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** A1114 ASN B 306 GLN B 902 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103706 restraints weight = 31068.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105541 restraints weight = 23039.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105651 restraints weight = 17964.601| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19148 Z= 0.161 Angle : 0.620 11.557 25857 Z= 0.326 Chirality : 0.044 0.218 2906 Planarity : 0.004 0.040 3305 Dihedral : 6.144 88.332 2530 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.57 % Favored : 91.26 % Rotamer: Outliers : 2.39 % Allowed : 11.45 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2334 helix: 0.64 (0.17), residues: 1055 sheet: -1.35 (0.32), residues: 254 loop : -1.80 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 186 HIS 0.011 0.001 HIS A 121 PHE 0.029 0.002 PHE A 226 TYR 0.017 0.001 TYR A 605 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 749) hydrogen bonds : angle 4.39505 ( 2058) metal coordination : bond 0.01182 ( 10) metal coordination : angle 2.46792 ( 3) covalent geometry : bond 0.00383 (19138) covalent geometry : angle 0.61994 (25854) *********************** 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 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4308 (ppp) cc_final: 0.4066 (ppp) REVERT: A 313 VAL cc_start: 0.9173 (t) cc_final: 0.8932 (p) REVERT: A 655 TYR cc_start: 0.8327 (m-80) cc_final: 0.8080 (m-10) REVERT: A 672 GLU cc_start: 0.8101 (tp30) cc_final: 0.7829 (tp30) REVERT: A 822 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 985 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 1131 MET cc_start: 0.7977 (tpp) cc_final: 0.7524 (mpp) REVERT: A 1176 MET cc_start: 0.8102 (tpp) cc_final: 0.7449 (tpp) REVERT: A 1241 ILE cc_start: 0.9069 (mm) cc_final: 0.8791 (mm) REVERT: B 235 MET cc_start: 0.7593 (ptp) cc_final: 0.7050 (tmm) REVERT: B 247 LEU cc_start: 0.7864 (mm) cc_final: 0.7400 (tp) REVERT: B 597 ASP cc_start: 0.8304 (m-30) cc_final: 0.8079 (m-30) REVERT: B 727 GLU cc_start: 0.7870 (mp0) cc_final: 0.7486 (tm-30) REVERT: B 775 MET cc_start: 0.6325 (ttt) cc_final: 0.5882 (ttt) REVERT: U 12 ASP cc_start: 0.8321 (t70) cc_final: 0.8006 (t0) REVERT: U 15 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7918 (tp-100) REVERT: U 40 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7862 (mp) REVERT: U 44 TYR cc_start: 0.8741 (t80) cc_final: 0.8475 (t80) outliers start: 50 outliers final: 35 residues processed: 222 average time/residue: 0.2754 time to fit residues: 99.3400 Evaluate side-chains 205 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 240 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU 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 471 GLU 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 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 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 244 LEU 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 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 895 SER 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 Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 108 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098836 restraints weight = 31310.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102139 restraints weight = 18881.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104300 restraints weight = 13852.505| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19148 Z= 0.185 Angle : 0.625 11.094 25857 Z= 0.326 Chirality : 0.044 0.228 2906 Planarity : 0.004 0.040 3305 Dihedral : 6.111 88.040 2530 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.74 % Favored : 91.09 % Rotamer: Outliers : 2.72 % Allowed : 11.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2334 helix: 0.67 (0.17), residues: 1054 sheet: -1.48 (0.33), residues: 249 loop : -1.87 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 186 HIS 0.015 0.001 HIS A 121 PHE 0.021 0.002 PHE A 226 TYR 0.018 0.002 TYR A 605 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 749) hydrogen bonds : angle 4.37086 ( 2058) metal coordination : bond 0.01280 ( 10) metal coordination : angle 2.16490 ( 3) covalent geometry : bond 0.00446 (19138) covalent geometry : angle 0.62483 (25854) *********************** 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 233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4438 (ppp) cc_final: 0.4179 (ppp) REVERT: A 248 ASP cc_start: 0.6809 (t0) cc_final: 0.6547 (t0) REVERT: A 313 VAL cc_start: 0.9239 (t) cc_final: 0.8999 (p) REVERT: A 655 TYR cc_start: 0.8347 (m-80) cc_final: 0.8103 (m-10) REVERT: A 672 GLU cc_start: 0.8046 (tp30) cc_final: 0.7802 (tp30) REVERT: A 822 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 985 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8156 (pp) REVERT: A 1131 MET cc_start: 0.8043 (tpp) cc_final: 0.7591 (mpp) REVERT: A 1176 MET cc_start: 0.8107 (tpp) cc_final: 0.7492 (tpp) REVERT: A 1241 ILE cc_start: 0.9143 (mm) cc_final: 0.8899 (mm) REVERT: B 235 MET cc_start: 0.7885 (ptp) cc_final: 0.7310 (tmm) REVERT: B 727 GLU cc_start: 0.7853 (mp0) cc_final: 0.7492 (tm-30) REVERT: U 12 ASP cc_start: 0.8373 (t70) cc_final: 0.8048 (t0) REVERT: U 15 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7957 (tp-100) REVERT: U 40 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7852 (mp) REVERT: U 44 TYR cc_start: 0.8774 (t80) cc_final: 0.8499 (t80) outliers start: 57 outliers final: 37 residues processed: 220 average time/residue: 0.2941 time to fit residues: 105.7759 Evaluate side-chains 206 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 256 ASN 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 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 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 813 HIS 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 243 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 895 SER 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 Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105602 restraints weight = 30646.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104209 restraints weight = 23880.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105450 restraints weight = 20091.033| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19148 Z= 0.137 Angle : 0.596 12.120 25857 Z= 0.309 Chirality : 0.043 0.204 2906 Planarity : 0.004 0.039 3305 Dihedral : 6.032 88.249 2530 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.74 % Favored : 91.09 % Rotamer: Outliers : 2.15 % Allowed : 12.55 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2334 helix: 0.85 (0.17), residues: 1045 sheet: -1.46 (0.33), residues: 249 loop : -1.82 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 186 HIS 0.012 0.001 HIS A 121 PHE 0.030 0.001 PHE B 972 TYR 0.016 0.001 TYR A 605 ARG 0.005 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 749) hydrogen bonds : angle 4.23608 ( 2058) metal coordination : bond 0.00899 ( 10) metal coordination : angle 2.13025 ( 3) covalent geometry : bond 0.00318 (19138) covalent geometry : angle 0.59521 (25854) *********************** 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 226 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4499 (ppp) cc_final: 0.4210 (ppp) REVERT: A 102 LEU cc_start: 0.8468 (tp) cc_final: 0.8239 (tt) REVERT: A 313 VAL cc_start: 0.9194 (t) cc_final: 0.8979 (p) REVERT: A 655 TYR cc_start: 0.8295 (m-80) cc_final: 0.8064 (m-10) REVERT: A 985 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8153 (pp) REVERT: A 1131 MET cc_start: 0.7987 (tpp) cc_final: 0.7514 (mpp) REVERT: A 1176 MET cc_start: 0.8240 (tpp) cc_final: 0.7633 (tpp) REVERT: A 1241 ILE cc_start: 0.9029 (mm) cc_final: 0.8736 (mm) REVERT: B 235 MET cc_start: 0.7588 (ptp) cc_final: 0.7079 (tmm) REVERT: B 727 GLU cc_start: 0.7973 (mp0) cc_final: 0.7540 (tm-30) REVERT: B 775 MET cc_start: 0.6543 (ttt) cc_final: 0.6117 (ttt) REVERT: B 888 TRP cc_start: 0.7618 (t60) cc_final: 0.7413 (t60) REVERT: B 917 TRP cc_start: 0.5826 (p-90) cc_final: 0.3866 (p-90) REVERT: U 12 ASP cc_start: 0.8311 (t70) cc_final: 0.8033 (t0) REVERT: U 15 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7911 (tp-100) REVERT: U 44 TYR cc_start: 0.8684 (t80) cc_final: 0.8283 (t80) REVERT: U 56 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8423 (ttmt) outliers start: 45 outliers final: 36 residues processed: 212 average time/residue: 0.2852 time to fit residues: 99.1918 Evaluate side-chains 208 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 419 MET Chi-restraints excluded: chain A residue 433 LEU 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 583 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 943 VAL 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 123 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE 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 517 CYS Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 1010 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 86 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 212 optimal weight: 0.0000 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.142550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102854 restraints weight = 31229.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103899 restraints weight = 22822.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104105 restraints weight = 19678.231| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19148 Z= 0.191 Angle : 0.631 11.082 25857 Z= 0.327 Chirality : 0.044 0.196 2906 Planarity : 0.004 0.041 3305 Dihedral : 6.065 88.263 2530 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.43 % Favored : 90.40 % Rotamer: Outliers : 2.24 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2334 helix: 0.81 (0.17), residues: 1046 sheet: -1.49 (0.33), residues: 248 loop : -1.88 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 186 HIS 0.012 0.001 HIS A 121 PHE 0.023 0.002 PHE B 972 TYR 0.018 0.002 TYR A 605 ARG 0.004 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 749) hydrogen bonds : angle 4.32851 ( 2058) metal coordination : bond 0.01227 ( 10) metal coordination : angle 1.93282 ( 3) covalent geometry : bond 0.00463 (19138) covalent geometry : angle 0.63064 (25854) *********************** 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 219 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4780 (ppp) cc_final: 0.4452 (ppp) REVERT: A 191 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7909 (mmtp) REVERT: A 313 VAL cc_start: 0.9232 (t) cc_final: 0.9021 (p) REVERT: A 655 TYR cc_start: 0.8338 (m-80) cc_final: 0.8109 (m-10) REVERT: A 841 MET cc_start: 0.8932 (mmm) cc_final: 0.8719 (mmm) REVERT: A 985 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8097 (pp) REVERT: A 1131 MET cc_start: 0.8032 (tpp) cc_final: 0.7551 (mpp) REVERT: A 1176 MET cc_start: 0.8165 (tpp) cc_final: 0.7625 (tpp) REVERT: A 1241 ILE cc_start: 0.9106 (mm) cc_final: 0.8829 (mm) REVERT: B 235 MET cc_start: 0.7416 (ptp) cc_final: 0.6693 (tmm) REVERT: B 727 GLU cc_start: 0.7812 (mp0) cc_final: 0.7536 (tm-30) REVERT: B 888 TRP cc_start: 0.7467 (t60) cc_final: 0.7171 (t60) REVERT: B 917 TRP cc_start: 0.5846 (p-90) cc_final: 0.3896 (p-90) REVERT: U 12 ASP cc_start: 0.8385 (t70) cc_final: 0.8122 (t0) REVERT: U 15 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7967 (tp-100) REVERT: U 40 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7891 (mp) REVERT: U 44 TYR cc_start: 0.8803 (t80) cc_final: 0.8414 (t80) outliers start: 47 outliers final: 38 residues processed: 212 average time/residue: 0.3541 time to fit residues: 123.7541 Evaluate side-chains 204 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 2.997 ------------------------------------------------------------------------------- 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 256 ASN 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 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 572 LEU 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 757 ILE Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 943 VAL 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 266 LYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue -1 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 Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 418 HIS A 463 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104397 restraints weight = 30980.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103105 restraints weight = 23377.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104403 restraints weight = 19200.990| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5298 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= 0.140 Angle : 0.600 11.070 25857 Z= 0.310 Chirality : 0.043 0.194 2906 Planarity : 0.004 0.038 3305 Dihedral : 5.993 88.626 2530 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.13 % Favored : 90.70 % Rotamer: Outliers : 2.29 % Allowed : 12.50 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2334 helix: 0.91 (0.17), residues: 1045 sheet: -1.49 (0.33), residues: 249 loop : -1.85 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 186 HIS 0.004 0.001 HIS A1129 PHE 0.023 0.001 PHE B 972 TYR 0.016 0.001 TYR A 605 ARG 0.004 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 749) hydrogen bonds : angle 4.18614 ( 2058) metal coordination : bond 0.00874 ( 10) metal coordination : angle 1.85609 ( 3) covalent geometry : bond 0.00330 (19138) covalent geometry : angle 0.59955 (25854) *********************** 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 225 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4745 (ppp) cc_final: 0.4418 (ppp) REVERT: A 60 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 313 VAL cc_start: 0.9197 (t) cc_final: 0.8965 (p) REVERT: A 655 TYR cc_start: 0.8277 (m-80) cc_final: 0.8038 (m-10) REVERT: A 841 MET cc_start: 0.8929 (mmm) cc_final: 0.8687 (mmm) REVERT: A 985 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8072 (pp) REVERT: A 1061 SER cc_start: 0.9171 (t) cc_final: 0.8659 (p) REVERT: A 1131 MET cc_start: 0.8001 (tpp) cc_final: 0.7498 (mpp) REVERT: A 1176 MET cc_start: 0.8205 (tpp) cc_final: 0.7705 (tpp) REVERT: A 1190 ASP cc_start: 0.6611 (t0) cc_final: 0.6312 (t0) REVERT: A 1241 ILE cc_start: 0.9049 (mm) cc_final: 0.8758 (mm) REVERT: B 235 MET cc_start: 0.7554 (ptp) cc_final: 0.6775 (tmm) REVERT: B 471 ASN cc_start: 0.8626 (m-40) cc_final: 0.8401 (t0) REVERT: B 727 GLU cc_start: 0.8027 (mp0) cc_final: 0.7584 (tm-30) REVERT: B 917 TRP cc_start: 0.5888 (p-90) cc_final: 0.3701 (p-90) REVERT: U 12 ASP cc_start: 0.8350 (t70) cc_final: 0.8067 (t0) REVERT: U 15 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8008 (tp-100) REVERT: U 44 TYR cc_start: 0.8705 (t80) cc_final: 0.8322 (t80) REVERT: U 56 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8396 (ttmt) outliers start: 48 outliers final: 35 residues processed: 213 average time/residue: 0.3262 time to fit residues: 113.8780 Evaluate side-chains 206 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU 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 256 ASN 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 471 GLU 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 757 ILE Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 943 VAL 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 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 85 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 28 optimal weight: 0.2980 chunk 135 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 chunk 147 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106420 restraints weight = 30706.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105317 restraints weight = 24419.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106392 restraints weight = 20100.550| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19148 Z= 0.116 Angle : 0.586 11.905 25857 Z= 0.301 Chirality : 0.043 0.307 2906 Planarity : 0.004 0.039 3305 Dihedral : 5.872 89.688 2530 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.87 % Favored : 91.09 % Rotamer: Outliers : 1.67 % Allowed : 13.26 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2334 helix: 1.07 (0.17), residues: 1036 sheet: -1.34 (0.34), residues: 246 loop : -1.83 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 186 HIS 0.007 0.001 HIS A 121 PHE 0.020 0.001 PHE B 972 TYR 0.018 0.001 TYR B 859 ARG 0.004 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 749) hydrogen bonds : angle 4.06153 ( 2058) metal coordination : bond 0.00777 ( 10) metal coordination : angle 2.04381 ( 3) covalent geometry : bond 0.00264 (19138) covalent geometry : angle 0.58562 (25854) ********************** 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 219 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4563 (ppp) cc_final: 0.4276 (ppp) REVERT: A 102 LEU cc_start: 0.8512 (tp) cc_final: 0.8295 (tt) REVERT: A 191 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7940 (mmtp) REVERT: A 203 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7698 (p) REVERT: A 313 VAL cc_start: 0.9170 (t) cc_final: 0.8953 (p) REVERT: A 655 TYR cc_start: 0.8252 (m-80) cc_final: 0.8030 (m-10) REVERT: A 985 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8044 (pp) REVERT: A 1061 SER cc_start: 0.9122 (t) cc_final: 0.8651 (p) REVERT: A 1131 MET cc_start: 0.7947 (tpp) cc_final: 0.7464 (mpp) REVERT: A 1176 MET cc_start: 0.8173 (tpp) cc_final: 0.7687 (tpp) REVERT: A 1190 ASP cc_start: 0.6514 (t0) cc_final: 0.6238 (t0) REVERT: A 1241 ILE cc_start: 0.8959 (mm) cc_final: 0.8642 (mm) REVERT: B 235 MET cc_start: 0.7472 (ptp) cc_final: 0.6714 (tmm) REVERT: B 727 GLU cc_start: 0.7973 (mp0) cc_final: 0.7584 (tm-30) REVERT: B 875 MET cc_start: 0.6440 (pmm) cc_final: 0.5970 (pmm) REVERT: B 917 TRP cc_start: 0.5960 (p-90) cc_final: 0.3831 (p-90) REVERT: U 12 ASP cc_start: 0.8304 (t70) cc_final: 0.8006 (t0) REVERT: U 15 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7965 (tp-100) REVERT: U 40 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7843 (mp) outliers start: 35 outliers final: 30 residues processed: 211 average time/residue: 0.2700 time to fit residues: 93.0863 Evaluate side-chains 195 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU 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 419 MET Chi-restraints excluded: chain A residue 433 LEU 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 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 936 THR 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 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 895 SER 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 Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 190 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 209 optimal weight: 0.0870 chunk 197 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 230 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105904 restraints weight = 30612.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106141 restraints weight = 22458.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106988 restraints weight = 19512.110| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19148 Z= 0.115 Angle : 0.586 13.683 25857 Z= 0.301 Chirality : 0.043 0.375 2906 Planarity : 0.004 0.041 3305 Dihedral : 5.797 87.600 2530 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.91 % Favored : 91.05 % Rotamer: Outliers : 1.81 % Allowed : 13.45 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2334 helix: 1.16 (0.17), residues: 1036 sheet: -1.37 (0.34), residues: 249 loop : -1.78 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 186 HIS 0.006 0.001 HIS A 121 PHE 0.018 0.001 PHE B 972 TYR 0.019 0.001 TYR U 37 ARG 0.004 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 749) hydrogen bonds : angle 4.04112 ( 2058) metal coordination : bond 0.00572 ( 10) metal coordination : angle 1.82181 ( 3) covalent geometry : bond 0.00260 (19138) covalent geometry : angle 0.58532 (25854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6105.07 seconds wall clock time: 110 minutes 6.94 seconds (6606.94 seconds total)