Starting phenix.real_space_refine on Tue Nov 19 08:39:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/11_2024/8fvu_29493_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/11_2024/8fvu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/11_2024/8fvu_29493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/11_2024/8fvu_29493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/11_2024/8fvu_29493_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvu_29493/11_2024/8fvu_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.73, per 1000 atoms: 0.57 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: 4.74 Conformation dependent library (CDL) restraints added in 2.4 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: 2.76 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: 8.11 Time building geometry restraints manager: 5.51 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: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 48.160 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.240 ------------------------------------------------------------------------------- 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 : 0.012 0.096 19138 Z= 0.761 Angle : 1.221 19.480 25854 Z= 0.848 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 *********************** 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 : 2.162 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: 0.3500 time to fit residues: 264.9978 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 : 2.096 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 19138 Z= 0.220 Angle : 0.696 12.272 25854 Z= 0.370 Chirality : 0.044 0.239 2906 Planarity : 0.004 0.041 3305 Dihedral : 5.799 80.865 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 *********************** 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 : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4899 (ppp) cc_final: 0.3971 (ppp) REVERT: A 323 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6807 (mm-30) REVERT: A 398 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8441 (tm-30) REVERT: A 1176 MET cc_start: 0.8214 (tpp) cc_final: 0.7769 (tpp) REVERT: A 1190 ASP cc_start: 0.7670 (t0) cc_final: 0.7206 (t70) REVERT: A 1363 SER cc_start: 0.9325 (m) cc_final: 0.9079 (p) REVERT: A 1401 ILE cc_start: 0.8265 (mm) cc_final: 0.7874 (mm) REVERT: B 125 ASP cc_start: 0.8405 (t0) cc_final: 0.8089 (t0) REVERT: B 235 MET cc_start: 0.7998 (ptp) cc_final: 0.7472 (mtp) REVERT: B 237 LEU cc_start: 0.7431 (mt) cc_final: 0.7220 (mt) REVERT: B 256 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7497 (mp10) REVERT: B 750 ARG cc_start: 0.7556 (pmt170) cc_final: 0.7288 (mtp180) REVERT: B 775 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7008 (ttt) REVERT: B 847 LEU cc_start: 0.7874 (tp) cc_final: 0.7283 (mp) REVERT: B 875 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6632 (ptp) REVERT: U 12 ASP cc_start: 0.8315 (t70) cc_final: 0.7925 (t0) REVERT: U 36 ASN cc_start: 0.8826 (m-40) cc_final: 0.8586 (m110) REVERT: U 40 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8231 (mp) outliers start: 45 outliers final: 25 residues processed: 310 average time/residue: 0.3175 time to fit residues: 153.1612 Evaluate side-chains 222 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 875 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 117 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 228 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN B 552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19138 Z= 0.272 Angle : 0.658 12.550 25854 Z= 0.346 Chirality : 0.045 0.197 2906 Planarity : 0.004 0.039 3305 Dihedral : 5.819 87.891 2530 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 2.19 % Allowed : 9.69 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.73 (0.18), residues: 2334 helix: 0.60 (0.17), residues: 1059 sheet: -0.68 (0.33), residues: 254 loop : -1.59 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 186 HIS 0.008 0.001 HIS A 121 PHE 0.021 0.002 PHE U 69 TYR 0.020 0.002 TYR U 37 ARG 0.006 0.000 ARG A1330 *********************** 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: 46 poor density : 214 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5053 (ppp) cc_final: 0.4491 (ppp) REVERT: A 398 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8326 (tm-30) REVERT: A 1170 PHE cc_start: 0.7588 (t80) cc_final: 0.7146 (t80) REVERT: A 1190 ASP cc_start: 0.7634 (t0) cc_final: 0.7210 (t70) REVERT: A 1206 ILE cc_start: 0.8117 (pt) cc_final: 0.7915 (tt) REVERT: B 235 MET cc_start: 0.7885 (ptp) cc_final: 0.7368 (mtp) REVERT: B 256 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7648 (mp10) REVERT: B 775 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6630 (ttt) REVERT: B 875 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6563 (ptp) REVERT: B 927 LEU cc_start: 0.8892 (mt) cc_final: 0.8650 (tp) REVERT: U 12 ASP cc_start: 0.8398 (t70) cc_final: 0.8063 (t0) REVERT: U 15 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8206 (tp-100) REVERT: U 40 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8264 (mp) outliers start: 46 outliers final: 29 residues processed: 248 average time/residue: 0.3041 time to fit residues: 119.2985 Evaluate side-chains 206 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 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 572 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 874 SER 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 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 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 209 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 0.0000 chunk 212 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 GLN ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19138 Z= 0.192 Angle : 0.595 12.659 25854 Z= 0.314 Chirality : 0.043 0.180 2906 Planarity : 0.004 0.050 3305 Dihedral : 5.769 88.435 2530 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 2.58 % Allowed : 10.35 % Favored : 87.07 % 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: 0.78 (0.17), residues: 1057 sheet: -0.91 (0.34), residues: 243 loop : -1.65 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 186 HIS 0.005 0.001 HIS A 121 PHE 0.017 0.001 PHE A 750 TYR 0.018 0.001 TYR U 37 ARG 0.003 0.000 ARG A 590 *********************** 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 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4883 (ppp) cc_final: 0.4324 (ppp) REVERT: A 822 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 931 PHE cc_start: 0.7628 (m-10) cc_final: 0.7216 (m-10) REVERT: A 985 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8174 (pp) REVERT: A 1190 ASP cc_start: 0.7636 (t0) cc_final: 0.7182 (t70) REVERT: B 235 MET cc_start: 0.7694 (ptp) cc_final: 0.7171 (mtp) REVERT: B 247 LEU cc_start: 0.7600 (mm) cc_final: 0.7088 (tp) REVERT: B 256 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7697 (mp10) REVERT: B 775 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6667 (ttt) REVERT: B 942 LEU cc_start: 0.7536 (tt) cc_final: 0.6992 (tp) REVERT: U 12 ASP cc_start: 0.8403 (t70) cc_final: 0.8071 (t0) REVERT: U 15 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8167 (tp-100) REVERT: U 40 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8201 (mp) outliers start: 54 outliers final: 39 residues processed: 234 average time/residue: 0.2739 time to fit residues: 102.8047 Evaluate side-chains 207 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 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 474 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 775 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 0.0770 chunk 127 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19138 Z= 0.249 Angle : 0.610 11.813 25854 Z= 0.321 Chirality : 0.044 0.226 2906 Planarity : 0.004 0.035 3305 Dihedral : 5.832 84.338 2530 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.40 % Favored : 91.47 % Rotamer: Outliers : 2.39 % Allowed : 11.31 % 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: -0.72 (0.18), residues: 2334 helix: 0.83 (0.17), residues: 1051 sheet: -1.12 (0.33), residues: 243 loop : -1.70 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 186 HIS 0.004 0.001 HIS A 930 PHE 0.017 0.002 PHE U 69 TYR 0.020 0.001 TYR A 605 ARG 0.003 0.000 ARG A1330 *********************** 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 224 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4906 (ppp) cc_final: 0.4636 (ppp) REVERT: A 822 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 985 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 1131 MET cc_start: 0.8596 (tpp) cc_final: 0.8283 (mpp) REVERT: A 1170 PHE cc_start: 0.7697 (t80) cc_final: 0.7405 (t80) REVERT: A 1176 MET cc_start: 0.8336 (tpp) cc_final: 0.7771 (tpp) REVERT: A 1190 ASP cc_start: 0.7538 (t0) cc_final: 0.7120 (t0) REVERT: A 1241 ILE cc_start: 0.9116 (mm) cc_final: 0.8859 (mm) REVERT: B 235 MET cc_start: 0.7649 (ptp) cc_final: 0.7115 (mtp) REVERT: B 247 LEU cc_start: 0.7719 (mm) cc_final: 0.7251 (tp) REVERT: B 256 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7935 (mp10) REVERT: B 597 ASP cc_start: 0.8386 (m-30) cc_final: 0.8174 (m-30) REVERT: B 795 LEU cc_start: 0.8332 (mp) cc_final: 0.7995 (mp) REVERT: U 12 ASP cc_start: 0.8472 (t70) cc_final: 0.8158 (t0) REVERT: U 15 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8265 (tp-100) REVERT: U 40 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8230 (mp) REVERT: U 44 TYR cc_start: 0.8994 (t80) cc_final: 0.8673 (t80) outliers start: 50 outliers final: 37 residues processed: 208 average time/residue: 0.2703 time to fit residues: 90.9770 Evaluate side-chains 203 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 187 optimal weight: 0.0770 chunk 104 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 463 ASN A 606 ASN A 651 HIS ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19138 Z= 0.299 Angle : 0.634 11.411 25854 Z= 0.331 Chirality : 0.045 0.245 2906 Planarity : 0.004 0.038 3305 Dihedral : 6.027 87.179 2530 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.91 % Favored : 90.92 % Rotamer: Outliers : 2.81 % Allowed : 11.26 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.18), residues: 2334 helix: 0.79 (0.17), residues: 1051 sheet: -1.34 (0.33), residues: 248 loop : -1.78 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 186 HIS 0.007 0.001 HIS A 121 PHE 0.030 0.002 PHE A 226 TYR 0.017 0.002 TYR U 37 ARG 0.003 0.000 ARG A1330 *********************** 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 236 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4980 (ppp) cc_final: 0.4749 (ppp) REVERT: A 822 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8133 (tm-30) REVERT: A 985 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 1131 MET cc_start: 0.8703 (tpp) cc_final: 0.8369 (mpp) REVERT: A 1176 MET cc_start: 0.8440 (tpp) cc_final: 0.7851 (tpp) REVERT: A 1190 ASP cc_start: 0.7595 (t0) cc_final: 0.7208 (t0) REVERT: A 1241 ILE cc_start: 0.9169 (mm) cc_final: 0.8910 (mm) REVERT: B 235 MET cc_start: 0.7551 (ptp) cc_final: 0.6979 (mtp) REVERT: B 256 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7893 (mp10) REVERT: U 12 ASP cc_start: 0.8544 (t70) cc_final: 0.8264 (t0) REVERT: U 15 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8282 (tp-100) REVERT: U 40 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8284 (mp) REVERT: U 44 TYR cc_start: 0.9043 (t80) cc_final: 0.8736 (t80) outliers start: 59 outliers final: 39 residues processed: 219 average time/residue: 0.2867 time to fit residues: 101.4749 Evaluate side-chains 204 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1020 LEU 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 331 LEU Chi-restraints excluded: chain B residue 445 SER 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 217 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 418 HIS A 463 ASN B 147 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19138 Z= 0.211 Angle : 0.585 10.810 25854 Z= 0.305 Chirality : 0.043 0.208 2906 Planarity : 0.004 0.037 3305 Dihedral : 5.919 86.692 2530 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.48 % Favored : 91.39 % Rotamer: Outliers : 2.15 % Allowed : 12.64 % 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: -0.73 (0.18), residues: 2334 helix: 0.93 (0.17), residues: 1052 sheet: -1.37 (0.33), residues: 248 loop : -1.77 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 186 HIS 0.012 0.001 HIS A 121 PHE 0.021 0.001 PHE A 226 TYR 0.017 0.001 TYR A 605 ARG 0.003 0.000 ARG A 585 *********************** 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 223 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4864 (ppp) cc_final: 0.4618 (ppp) REVERT: A 672 GLU cc_start: 0.8570 (tp30) cc_final: 0.8194 (tp30) REVERT: A 725 MET cc_start: 0.8604 (mmp) cc_final: 0.8393 (mmt) REVERT: A 822 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 985 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8285 (pp) REVERT: A 1131 MET cc_start: 0.8671 (tpp) cc_final: 0.8339 (mpp) REVERT: A 1170 PHE cc_start: 0.7804 (t80) cc_final: 0.7448 (t80) REVERT: A 1176 MET cc_start: 0.8404 (tpp) cc_final: 0.7842 (tpp) REVERT: A 1190 ASP cc_start: 0.7518 (t0) cc_final: 0.7144 (t0) REVERT: B 235 MET cc_start: 0.7395 (ptp) cc_final: 0.6910 (tmm) REVERT: B 256 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7887 (mp10) REVERT: B 715 TYR cc_start: 0.8056 (p90) cc_final: 0.7854 (p90) REVERT: B 917 TRP cc_start: 0.5852 (p-90) cc_final: 0.4344 (p-90) REVERT: U 12 ASP cc_start: 0.8453 (t70) cc_final: 0.8168 (t0) REVERT: U 15 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8242 (tp-100) REVERT: U 44 TYR cc_start: 0.8989 (t80) cc_final: 0.8591 (t80) outliers start: 45 outliers final: 33 residues processed: 213 average time/residue: 0.3156 time to fit residues: 110.3427 Evaluate side-chains 195 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 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 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 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 331 LEU Chi-restraints excluded: chain B residue 445 SER 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 61 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 134 optimal weight: 0.0470 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 0.0000 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN B 147 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN U 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19138 Z= 0.235 Angle : 0.604 10.428 25854 Z= 0.313 Chirality : 0.044 0.195 2906 Planarity : 0.004 0.036 3305 Dihedral : 5.896 85.730 2530 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.95 % Favored : 90.92 % Rotamer: Outliers : 1.96 % Allowed : 12.83 % 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: -0.71 (0.18), residues: 2334 helix: 0.97 (0.17), residues: 1046 sheet: -1.36 (0.33), residues: 253 loop : -1.78 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 186 HIS 0.015 0.001 HIS A 121 PHE 0.021 0.001 PHE A 226 TYR 0.017 0.001 TYR A 605 ARG 0.002 0.000 ARG A 585 *********************** 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 211 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4965 (ppp) cc_final: 0.4145 (ppp) REVERT: A 672 GLU cc_start: 0.8625 (tp30) cc_final: 0.8421 (tp30) REVERT: A 822 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 985 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8289 (pp) REVERT: A 1061 SER cc_start: 0.9303 (t) cc_final: 0.8858 (p) REVERT: A 1131 MET cc_start: 0.8706 (tpp) cc_final: 0.8387 (mpp) REVERT: A 1170 PHE cc_start: 0.7936 (t80) cc_final: 0.7699 (t80) REVERT: A 1176 MET cc_start: 0.8429 (tpp) cc_final: 0.7828 (tpp) REVERT: A 1190 ASP cc_start: 0.7481 (t0) cc_final: 0.7107 (t0) REVERT: B 235 MET cc_start: 0.7368 (ptp) cc_final: 0.6909 (tmm) REVERT: B 256 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7866 (mp10) REVERT: B 715 TYR cc_start: 0.8104 (p90) cc_final: 0.7876 (p90) REVERT: B 917 TRP cc_start: 0.5817 (p-90) cc_final: 0.4123 (p-90) REVERT: U 12 ASP cc_start: 0.8508 (t70) cc_final: 0.8221 (t0) REVERT: U 15 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8283 (tp-100) REVERT: U 40 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8239 (mp) REVERT: U 44 TYR cc_start: 0.9008 (t80) cc_final: 0.8665 (t80) outliers start: 41 outliers final: 35 residues processed: 202 average time/residue: 0.2875 time to fit residues: 93.7201 Evaluate side-chains 198 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 332 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19138 Z= 0.257 Angle : 0.610 10.286 25854 Z= 0.316 Chirality : 0.044 0.193 2906 Planarity : 0.004 0.037 3305 Dihedral : 5.901 86.804 2530 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.38 % Favored : 90.53 % Rotamer: Outliers : 2.00 % Allowed : 12.98 % Favored : 85.02 % 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: -0.73 (0.18), residues: 2334 helix: 0.95 (0.17), residues: 1051 sheet: -1.38 (0.33), residues: 253 loop : -1.80 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B 186 HIS 0.016 0.001 HIS A 121 PHE 0.020 0.001 PHE A 226 TYR 0.017 0.001 TYR A 605 ARG 0.010 0.000 ARG B 148 *********************** 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 207 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4912 (ppp) cc_final: 0.4011 (ppp) REVERT: A 584 ASN cc_start: 0.8829 (m-40) cc_final: 0.8607 (m110) REVERT: A 822 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 985 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8275 (pp) REVERT: A 1061 SER cc_start: 0.9297 (t) cc_final: 0.8939 (p) REVERT: A 1131 MET cc_start: 0.8727 (tpp) cc_final: 0.8405 (mpp) REVERT: A 1174 MET cc_start: 0.8694 (tpp) cc_final: 0.8253 (tpp) REVERT: A 1176 MET cc_start: 0.8449 (tpp) cc_final: 0.7886 (tpp) REVERT: A 1190 ASP cc_start: 0.7485 (t0) cc_final: 0.7117 (t0) REVERT: A 1241 ILE cc_start: 0.9154 (mm) cc_final: 0.8864 (mm) REVERT: B 235 MET cc_start: 0.7353 (ptp) cc_final: 0.6903 (tmm) REVERT: B 256 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7771 (mp10) REVERT: B 715 TYR cc_start: 0.8116 (p90) cc_final: 0.7878 (p90) REVERT: B 775 MET cc_start: 0.7166 (tpp) cc_final: 0.6910 (ttt) REVERT: B 917 TRP cc_start: 0.5878 (p-90) cc_final: 0.4148 (p-90) REVERT: U 12 ASP cc_start: 0.8535 (t70) cc_final: 0.8241 (t0) REVERT: U 15 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8286 (tp-100) REVERT: U 40 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8264 (mp) REVERT: U 44 TYR cc_start: 0.9022 (t80) cc_final: 0.8624 (t80) outliers start: 42 outliers final: 36 residues processed: 196 average time/residue: 0.2889 time to fit residues: 91.9087 Evaluate side-chains 200 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 chunk 213 optimal weight: 0.0970 chunk 184 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 147 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 552 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19138 Z= 0.172 Angle : 0.569 10.206 25854 Z= 0.296 Chirality : 0.042 0.196 2906 Planarity : 0.003 0.035 3305 Dihedral : 5.755 86.795 2530 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.35 % Rotamer: Outliers : 1.81 % Allowed : 13.07 % Favored : 85.11 % 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: 1.14 (0.17), residues: 1042 sheet: -1.34 (0.33), residues: 255 loop : -1.78 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 186 HIS 0.004 0.001 HIS A 121 PHE 0.019 0.001 PHE A 226 TYR 0.014 0.001 TYR B 594 ARG 0.003 0.000 ARG A 167 ********************** 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 210 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4782 (ppp) cc_final: 0.4092 (ppp) REVERT: A 822 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 985 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 1061 SER cc_start: 0.9274 (t) cc_final: 0.8937 (p) REVERT: A 1131 MET cc_start: 0.8669 (tpp) cc_final: 0.8305 (mpp) REVERT: A 1174 MET cc_start: 0.8633 (tpp) cc_final: 0.8261 (tpp) REVERT: A 1176 MET cc_start: 0.8396 (tpp) cc_final: 0.7909 (tpp) REVERT: A 1190 ASP cc_start: 0.7488 (t0) cc_final: 0.7141 (t0) REVERT: B 235 MET cc_start: 0.7218 (ptp) cc_final: 0.6787 (tmm) REVERT: B 241 GLN cc_start: 0.7446 (pp30) cc_final: 0.7234 (pp30) REVERT: B 256 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7776 (mp10) REVERT: B 388 ARG cc_start: 0.9031 (mtp180) cc_final: 0.8588 (ttm110) REVERT: B 715 TYR cc_start: 0.8093 (p90) cc_final: 0.7871 (p90) REVERT: B 875 MET cc_start: 0.6190 (pmm) cc_final: 0.5842 (pmm) REVERT: B 917 TRP cc_start: 0.5909 (p-90) cc_final: 0.4016 (p-90) REVERT: B 958 MET cc_start: 0.6583 (mmp) cc_final: 0.6361 (mmp) REVERT: U 12 ASP cc_start: 0.8480 (t70) cc_final: 0.8167 (t0) REVERT: U 15 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8317 (tp-100) outliers start: 38 outliers final: 31 residues processed: 200 average time/residue: 0.2864 time to fit residues: 91.8809 Evaluate side-chains 196 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 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 813 HIS Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 615 ASP 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 61 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 170 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 185 optimal weight: 0.0670 chunk 77 optimal weight: 0.1980 chunk 190 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.2414 ------------------------------------------------------------------------------- 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 ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107661 restraints weight = 30985.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108536 restraints weight = 20396.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109667 restraints weight = 15455.473| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19138 Z= 0.142 Angle : 0.560 10.198 25854 Z= 0.291 Chirality : 0.042 0.201 2906 Planarity : 0.003 0.036 3305 Dihedral : 5.602 86.518 2530 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.10 % Favored : 91.82 % Rotamer: Outliers : 1.57 % Allowed : 13.74 % Favored : 84.69 % 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: -0.44 (0.19), residues: 2334 helix: 1.29 (0.17), residues: 1037 sheet: -1.24 (0.34), residues: 255 loop : -1.71 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 186 HIS 0.011 0.001 HIS A 121 PHE 0.019 0.001 PHE A 226 TYR 0.022 0.001 TYR B 367 ARG 0.004 0.000 ARG B 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.34 seconds wall clock time: 66 minutes 45.76 seconds (4005.76 seconds total)