Starting phenix.real_space_refine on Thu Aug 6 10:16:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yih_39319/08_2026/8yih_39319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yih_39319/08_2026/8yih_39319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yih_39319/08_2026/8yih_39319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yih_39319/08_2026/8yih_39319.map" model { file = "/net/cci-nas-00/data/ceres_data/8yih_39319/08_2026/8yih_39319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yih_39319/08_2026/8yih_39319.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 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 P 98 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 9018 2.51 5 N 2510 2.21 5 O 2996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14692 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 12490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 12490 Classifications: {'peptide': 1544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 63, 'TRANS': 1480} Chain breaks: 2 Chain: "C" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2029 Classifications: {'RNA': 96} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 46, 'rna3p_pyr': 48} Link IDs: {'rna2p': 2, 'rna3p': 93} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.54, per 1000 atoms: 0.24 Number of scatterers: 14692 At special positions: 0 Unit cell: (97.7522, 95.6038, 172.946, 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) S 68 16.00 P 98 15.00 Mg 2 11.99 O 2996 8.00 N 2510 7.00 C 9018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 679.4 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 11 sheets defined 55.1% alpha, 8.8% beta 35 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.610A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.525A pdb=" N ARG A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.997A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.912A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.559A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.047A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.587A pdb=" N MET A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.519A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 Processing helix chain 'A' and resid 293 through 314 removed outlier: 4.280A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.790A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.648A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 534 removed outlier: 3.603A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.628A pdb=" N ARG A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.679A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 removed outlier: 4.332A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 916 through 930 removed outlier: 7.087A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 4.041A pdb=" N ALA A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.644A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1016 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.687A pdb=" N ASN A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 removed outlier: 3.639A pdb=" N PHE A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 4.157A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 removed outlier: 3.534A pdb=" N LEU A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.880A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1261 No H-bonds generated for 'chain 'A' and resid 1260 through 1261' Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.588A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1293 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.730A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.762A pdb=" N LEU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1337 Processing helix chain 'A' and resid 1338 through 1341 Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1362 through 1382 removed outlier: 3.737A pdb=" N ILE A1366 " --> pdb=" O PRO A1362 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A1371 " --> pdb=" O ALA A1367 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A1381 " --> pdb=" O ILE A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 4.101A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1416 through 1420 Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 3.623A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.653A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1455 removed outlier: 4.456A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 4.104A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 removed outlier: 4.385A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.643A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 3.874A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1657 through 1662 Processing helix chain 'A' and resid 1701 through 1722 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.732A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 170 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 5.758A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR A 506 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 223 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYS A 388 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 390 " --> pdb=" O CYS A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.668A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.581A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.581A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.739A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 894 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 883 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1669 through 1670 removed outlier: 3.964A pdb=" N CYS A1684 " --> pdb=" O VAL A1695 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A1695 " --> pdb=" O CYS A1684 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1674 through 1676 removed outlier: 3.760A pdb=" N ILE A1674 " --> pdb=" O MET A1681 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A1681 " --> pdb=" O ILE A1674 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4438 1.34 - 1.46: 3908 1.46 - 1.58: 6554 1.58 - 1.70: 194 1.70 - 1.83: 106 Bond restraints: 15200 Sorted by residual: bond pdb=" CG PRO A 872 " pdb=" CD PRO A 872 " ideal model delta sigma weight residual 1.503 1.363 0.140 3.40e-02 8.65e+02 1.69e+01 bond pdb=" N1 U C 54 " pdb=" C2 U C 54 " ideal model delta sigma weight residual 1.381 1.396 -0.015 9.00e-03 1.23e+04 2.70e+00 bond pdb=" C1' U C 46 " pdb=" N1 U C 46 " ideal model delta sigma weight residual 1.464 1.486 -0.022 1.40e-02 5.10e+03 2.50e+00 bond pdb=" CB PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CA GLU A 541 " pdb=" CB GLU A 541 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.97e+00 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20820 2.69 - 5.39: 175 5.39 - 8.08: 17 8.08 - 10.77: 8 10.77 - 13.47: 4 Bond angle restraints: 21024 Sorted by residual: angle pdb=" N PRO A 872 " pdb=" CD PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 103.20 89.73 13.47 1.50e+00 4.44e-01 8.06e+01 angle pdb=" CA PRO A 872 " pdb=" N PRO A 872 " pdb=" CD PRO A 872 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 angle pdb=" N3 C C 11 " pdb=" C4 C C 11 " pdb=" N4 C C 11 " ideal model delta sigma weight residual 118.00 113.43 4.57 7.00e-01 2.04e+00 4.27e+01 angle pdb=" N4 C C 11 " pdb=" C4 C C 11 " pdb=" C5 C C 11 " ideal model delta sigma weight residual 120.20 124.69 -4.49 7.00e-01 2.04e+00 4.12e+01 angle pdb=" C5 G C 84 " pdb=" C6 G C 84 " pdb=" O6 G C 84 " ideal model delta sigma weight residual 128.60 124.91 3.69 6.00e-01 2.78e+00 3.78e+01 ... (remaining 21019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.70: 8656 29.70 - 59.39: 534 59.39 - 89.09: 94 89.09 - 118.79: 3 118.79 - 148.48: 1 Dihedral angle restraints: 9288 sinusoidal: 4691 harmonic: 4597 Sorted by residual: dihedral pdb=" C5' U C 46 " pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" O3' U C 46 " ideal model delta sinusoidal sigma weight residual 147.00 82.64 64.36 1 8.00e+00 1.56e-02 8.51e+01 dihedral pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " pdb=" C1' U C 46 " ideal model delta sinusoidal sigma weight residual -35.00 25.21 -60.21 1 8.00e+00 1.56e-02 7.55e+01 dihedral pdb=" O4' U C 46 " pdb=" C4' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " ideal model delta sinusoidal sigma weight residual 24.00 -32.57 56.57 1 8.00e+00 1.56e-02 6.74e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2011 0.057 - 0.114: 305 0.114 - 0.171: 123 0.171 - 0.228: 0 0.228 - 0.285: 1 Chirality restraints: 2440 Sorted by residual: chirality pdb=" C3' U C 46 " pdb=" C4' U C 46 " pdb=" O3' U C 46 " pdb=" C2' U C 46 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' C C 91 " pdb=" C4' C C 91 " pdb=" O3' C C 91 " pdb=" C2' C C 91 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" C1' U C 46 " pdb=" O4' U C 46 " pdb=" C2' U C 46 " pdb=" N1 U C 46 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2437 not shown) Planarity restraints: 2335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 370 " 0.014 2.00e-02 2.50e+03 1.78e-02 5.57e+00 pdb=" CG PHE A 370 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 370 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 370 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 370 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 370 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 582 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 583 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 904 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.025 5.00e-02 4.00e+02 ... (remaining 2332 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 169 2.51 - 3.11: 11311 3.11 - 3.70: 26054 3.70 - 4.30: 34304 4.30 - 4.90: 51635 Nonbonded interactions: 123473 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O3B ADP A1802 " model vdw 1.910 2.170 nonbonded pdb=" O2' U C 46 " pdb=" O5' U C 47 " model vdw 2.133 3.040 nonbonded pdb=" O LYS A1402 " pdb=" OG1 THR A1405 " model vdw 2.143 3.040 nonbonded pdb=" O PHE A 370 " pdb=" OG SER A 373 " model vdw 2.150 3.040 nonbonded pdb=" O LYS A 696 " pdb=" O2' G C 75 " model vdw 2.188 3.040 ... (remaining 123468 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.003 0.140 15200 Z= 0.167 Angle : 0.697 13.468 21024 Z= 0.435 Chirality : 0.047 0.285 2440 Planarity : 0.004 0.047 2335 Dihedral : 18.401 148.482 6306 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 21.75 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.22), residues: 1552 helix: 0.90 (0.20), residues: 712 sheet: -1.24 (0.37), residues: 167 loop : -0.69 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1658 TYR 0.010 0.001 TYR A 286 PHE 0.041 0.001 PHE A 370 TRP 0.020 0.001 TRP A1634 HIS 0.004 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (15200) covalent geometry : angle 0.69737 / 0.43 (21024) hydrogen bonds : bond 0.15128 / 9.78 ( 658) hydrogen bonds : angle 6.21107 / 4.42 ( 1802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 MET cc_start: 0.9342 (tpp) cc_final: 0.9047 (mmm) REVERT: A 1479 LEU cc_start: 0.9147 (tp) cc_final: 0.8811 (pp) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1081 time to fit residues: 13.2309 Evaluate side-chains 71 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 407 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 ASN ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 HIS ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.066346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047536 restraints weight = 90998.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049031 restraints weight = 51076.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049973 restraints weight = 35537.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050586 restraints weight = 28529.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.050969 restraints weight = 24865.362| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15200 Z= 0.227 Angle : 0.658 8.613 21024 Z= 0.342 Chirality : 0.043 0.285 2440 Planarity : 0.005 0.066 2335 Dihedral : 16.432 127.275 3159 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 0.07 % Allowed : 5.78 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1552 helix: 0.65 (0.19), residues: 722 sheet: -1.40 (0.36), residues: 167 loop : -0.74 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 416 TYR 0.023 0.002 TYR A 578 PHE 0.018 0.002 PHE A 119 TRP 0.014 0.002 TRP A 97 HIS 0.011 0.002 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (15200) covalent geometry : angle 0.65772 / 0.34 (21024) hydrogen bonds : bond 0.05122 / 3.33 ( 658) hydrogen bonds : angle 5.23037 / 3.63 ( 1802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8936 (tpt) cc_final: 0.8628 (tpt) REVERT: A 458 MET cc_start: 0.8869 (tpp) cc_final: 0.8658 (tpp) REVERT: A 922 MET cc_start: 0.8146 (mmp) cc_final: 0.7872 (mmm) REVERT: A 1389 MET cc_start: 0.9251 (tpp) cc_final: 0.8917 (mmm) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1038 time to fit residues: 15.3440 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 323 HIS A 550 HIS A 569 ASN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.067868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048959 restraints weight = 89939.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.050521 restraints weight = 50527.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051520 restraints weight = 35053.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052127 restraints weight = 27951.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052436 restraints weight = 24393.659| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15200 Z= 0.128 Angle : 0.570 8.822 21024 Z= 0.296 Chirality : 0.040 0.254 2440 Planarity : 0.004 0.050 2335 Dihedral : 16.243 131.816 3159 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1552 helix: 0.63 (0.19), residues: 729 sheet: -1.27 (0.37), residues: 167 loop : -0.72 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.017 0.002 TYR A1624 PHE 0.010 0.001 PHE A1001 TRP 0.014 0.001 TRP A 102 HIS 0.011 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15200) covalent geometry : angle 0.56971 / 0.30 (21024) hydrogen bonds : bond 0.04296 / 2.83 ( 658) hydrogen bonds : angle 4.80648 / 3.33 ( 1802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8139 (ppp) cc_final: 0.7856 (ppp) REVERT: A 458 MET cc_start: 0.8873 (tpp) cc_final: 0.8584 (tpp) REVERT: A 543 GLU cc_start: 0.7352 (mp0) cc_final: 0.6999 (mp0) REVERT: A 999 MET cc_start: 0.9074 (ptm) cc_final: 0.8704 (ppp) REVERT: A 1479 LEU cc_start: 0.9015 (tp) cc_final: 0.8786 (pp) REVERT: A 1511 THR cc_start: 0.9503 (p) cc_final: 0.9255 (t) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1094 time to fit residues: 18.4308 Evaluate side-chains 77 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 44 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 56 optimal weight: 0.0270 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 550 HIS ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.068212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049202 restraints weight = 89134.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050795 restraints weight = 49752.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051827 restraints weight = 34202.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052475 restraints weight = 27048.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052794 restraints weight = 23526.795| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15200 Z= 0.112 Angle : 0.550 8.369 21024 Z= 0.285 Chirality : 0.039 0.254 2440 Planarity : 0.004 0.052 2335 Dihedral : 16.116 133.186 3159 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1552 helix: 0.55 (0.19), residues: 735 sheet: -1.16 (0.37), residues: 167 loop : -0.65 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 627 TYR 0.015 0.001 TYR A 402 PHE 0.010 0.001 PHE A1641 TRP 0.013 0.001 TRP A 102 HIS 0.007 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15200) covalent geometry : angle 0.54984 / 0.29 (21024) hydrogen bonds : bond 0.04008 / 2.66 ( 658) hydrogen bonds : angle 4.63068 / 3.20 ( 1802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8477 (tmm) cc_final: 0.8249 (tmm) REVERT: A 322 MET cc_start: 0.8254 (ppp) cc_final: 0.7969 (ppp) REVERT: A 458 MET cc_start: 0.8803 (tpp) cc_final: 0.8526 (tpp) REVERT: A 543 GLU cc_start: 0.7428 (mp0) cc_final: 0.7050 (mp0) REVERT: A 620 MET cc_start: 0.8694 (tpt) cc_final: 0.8431 (mmm) REVERT: A 999 MET cc_start: 0.9086 (ptm) cc_final: 0.8707 (ppp) REVERT: A 1389 MET cc_start: 0.9463 (mmm) cc_final: 0.8704 (mmt) REVERT: A 1393 PHE cc_start: 0.8777 (m-80) cc_final: 0.8562 (m-80) REVERT: A 1479 LEU cc_start: 0.8957 (tp) cc_final: 0.8745 (pp) REVERT: A 1511 THR cc_start: 0.9541 (p) cc_final: 0.9296 (t) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.0946 time to fit residues: 16.3103 Evaluate side-chains 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 162 optimal weight: 50.0000 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 335 HIS A 490 GLN A 550 HIS ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.063973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.045416 restraints weight = 92315.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.046737 restraints weight = 54421.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047588 restraints weight = 38942.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048120 restraints weight = 31735.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.048435 restraints weight = 28093.914| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 15200 Z= 0.385 Angle : 0.859 12.420 21024 Z= 0.437 Chirality : 0.048 0.251 2440 Planarity : 0.006 0.103 2335 Dihedral : 16.370 139.660 3159 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1552 helix: 0.19 (0.19), residues: 720 sheet: -1.34 (0.40), residues: 145 loop : -1.02 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 167 TYR 0.032 0.003 TYR A 952 PHE 0.023 0.003 PHE A1219 TRP 0.010 0.002 TRP A 102 HIS 0.014 0.003 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.39 (15200) covalent geometry : angle 0.85920 / 0.44 (21024) hydrogen bonds : bond 0.05863 / 3.79 ( 658) hydrogen bonds : angle 5.30003 / 3.65 ( 1802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8812 (tpp) cc_final: 0.8561 (tpp) REVERT: A 620 MET cc_start: 0.8989 (tpt) cc_final: 0.8666 (tmm) REVERT: A 862 ASN cc_start: 0.8399 (t0) cc_final: 0.7994 (t0) REVERT: A 914 ASP cc_start: 0.7764 (t70) cc_final: 0.7318 (m-30) REVERT: A 1389 MET cc_start: 0.9365 (mmm) cc_final: 0.9157 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1093 time to fit residues: 12.7337 Evaluate side-chains 60 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 50.0000 chunk 89 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 490 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.065690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046857 restraints weight = 90294.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048319 restraints weight = 51383.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049263 restraints weight = 36013.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049856 restraints weight = 28887.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050195 restraints weight = 25320.370| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15200 Z= 0.176 Angle : 0.612 7.603 21024 Z= 0.321 Chirality : 0.041 0.259 2440 Planarity : 0.005 0.049 2335 Dihedral : 16.409 142.026 3159 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1552 helix: 0.43 (0.19), residues: 724 sheet: -1.42 (0.38), residues: 156 loop : -0.83 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 167 TYR 0.017 0.002 TYR A1624 PHE 0.013 0.001 PHE A1219 TRP 0.012 0.001 TRP A1634 HIS 0.008 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (15200) covalent geometry : angle 0.61213 / 0.32 (21024) hydrogen bonds : bond 0.04507 / 2.96 ( 658) hydrogen bonds : angle 4.86777 / 3.36 ( 1802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9685 (mmm) cc_final: 0.9452 (mmm) REVERT: A 458 MET cc_start: 0.8892 (tpp) cc_final: 0.8611 (tpp) REVERT: A 620 MET cc_start: 0.8862 (tpt) cc_final: 0.8510 (tmm) REVERT: A 862 ASN cc_start: 0.8398 (t0) cc_final: 0.8046 (t0) REVERT: A 914 ASP cc_start: 0.7493 (t70) cc_final: 0.7085 (m-30) REVERT: A 1389 MET cc_start: 0.9330 (mmm) cc_final: 0.9096 (mmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1003 time to fit residues: 13.2995 Evaluate side-chains 69 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 0.0470 chunk 162 optimal weight: 50.0000 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.065985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047236 restraints weight = 89829.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048659 restraints weight = 52079.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.049595 restraints weight = 36780.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.050190 restraints weight = 29675.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050463 restraints weight = 26039.563| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15200 Z= 0.160 Angle : 0.595 9.534 21024 Z= 0.310 Chirality : 0.041 0.257 2440 Planarity : 0.004 0.051 2335 Dihedral : 16.370 146.504 3159 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1552 helix: 0.53 (0.19), residues: 727 sheet: -1.15 (0.40), residues: 145 loop : -0.83 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.014 0.001 TYR A1624 PHE 0.011 0.001 PHE A1219 TRP 0.013 0.001 TRP A1634 HIS 0.007 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (15200) covalent geometry : angle 0.59470 / 0.31 (21024) hydrogen bonds : bond 0.04278 / 2.82 ( 658) hydrogen bonds : angle 4.72805 / 3.27 ( 1802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8481 (tmm) cc_final: 0.8181 (tmm) REVERT: A 322 MET cc_start: 0.8089 (ppp) cc_final: 0.7791 (ppp) REVERT: A 458 MET cc_start: 0.8835 (tpp) cc_final: 0.8542 (tpp) REVERT: A 620 MET cc_start: 0.8818 (tpt) cc_final: 0.8469 (mmm) REVERT: A 862 ASN cc_start: 0.8420 (t0) cc_final: 0.8056 (t0) REVERT: A 1389 MET cc_start: 0.9307 (mmm) cc_final: 0.9099 (mmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1103 time to fit residues: 14.8335 Evaluate side-chains 67 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 163 optimal weight: 50.0000 chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.065742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.046996 restraints weight = 89962.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048397 restraints weight = 52061.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049338 restraints weight = 36914.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049920 restraints weight = 29755.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050194 restraints weight = 26126.160| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15200 Z= 0.173 Angle : 0.605 12.038 21024 Z= 0.312 Chirality : 0.041 0.257 2440 Planarity : 0.004 0.050 2335 Dihedral : 16.364 151.020 3159 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1552 helix: 0.53 (0.19), residues: 733 sheet: -1.16 (0.40), residues: 145 loop : -0.81 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 627 TYR 0.019 0.002 TYR A1037 PHE 0.011 0.001 PHE A1219 TRP 0.013 0.001 TRP A1634 HIS 0.007 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15200) covalent geometry : angle 0.60526 / 0.31 (21024) hydrogen bonds : bond 0.04277 / 2.83 ( 658) hydrogen bonds : angle 4.70736 / 3.26 ( 1802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9672 (mmm) cc_final: 0.9435 (mmm) REVERT: A 222 MET cc_start: 0.8484 (tmm) cc_final: 0.8168 (tmm) REVERT: A 458 MET cc_start: 0.8837 (tpp) cc_final: 0.8543 (tpp) REVERT: A 543 GLU cc_start: 0.7420 (mp0) cc_final: 0.7055 (mp0) REVERT: A 620 MET cc_start: 0.8833 (tpt) cc_final: 0.8408 (mmm) REVERT: A 862 ASN cc_start: 0.8529 (t0) cc_final: 0.8177 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0969 time to fit residues: 12.8414 Evaluate side-chains 64 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 1 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 407 ASN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.066500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047597 restraints weight = 89299.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049046 restraints weight = 51843.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.049992 restraints weight = 36696.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050576 restraints weight = 29598.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050954 restraints weight = 26004.615| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15200 Z= 0.132 Angle : 0.582 7.758 21024 Z= 0.300 Chirality : 0.040 0.258 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.335 155.254 3159 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1552 helix: 0.60 (0.19), residues: 731 sheet: -1.06 (0.40), residues: 145 loop : -0.78 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 627 TYR 0.013 0.001 TYR A1624 PHE 0.036 0.001 PHE A1387 TRP 0.014 0.001 TRP A1634 HIS 0.005 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15200) covalent geometry : angle 0.58183 / 0.30 (21024) hydrogen bonds : bond 0.04050 / 2.69 ( 658) hydrogen bonds : angle 4.63325 / 3.21 ( 1802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9660 (mmm) cc_final: 0.9422 (mmm) REVERT: A 222 MET cc_start: 0.8487 (tmm) cc_final: 0.8161 (tmm) REVERT: A 322 MET cc_start: 0.8148 (ppp) cc_final: 0.7876 (ppp) REVERT: A 458 MET cc_start: 0.8820 (tpp) cc_final: 0.8507 (tpp) REVERT: A 543 GLU cc_start: 0.7411 (mp0) cc_final: 0.7057 (mp0) REVERT: A 620 MET cc_start: 0.8757 (tpt) cc_final: 0.8325 (mmm) REVERT: A 862 ASN cc_start: 0.8482 (t0) cc_final: 0.8109 (t0) REVERT: A 922 MET cc_start: 0.8185 (mmp) cc_final: 0.7911 (mmm) REVERT: A 1389 MET cc_start: 0.9440 (mmm) cc_final: 0.9137 (mmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1057 time to fit residues: 14.5989 Evaluate side-chains 70 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 81 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 126 optimal weight: 0.0070 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.066075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047291 restraints weight = 88876.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048688 restraints weight = 52070.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049588 restraints weight = 37089.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.050129 restraints weight = 30042.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050321 restraints weight = 26608.522| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15200 Z= 0.173 Angle : 0.608 7.400 21024 Z= 0.314 Chirality : 0.041 0.256 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.354 159.619 3159 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1552 helix: 0.55 (0.19), residues: 730 sheet: -1.15 (0.40), residues: 145 loop : -0.87 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 627 TYR 0.014 0.002 TYR A1624 PHE 0.028 0.002 PHE A1387 TRP 0.013 0.001 TRP A1634 HIS 0.008 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15200) covalent geometry : angle 0.60835 / 0.31 (21024) hydrogen bonds : bond 0.04186 / 2.76 ( 658) hydrogen bonds : angle 4.65659 / 3.22 ( 1802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9667 (mmm) cc_final: 0.9432 (mmm) REVERT: A 222 MET cc_start: 0.8483 (tmm) cc_final: 0.8151 (tmm) REVERT: A 322 MET cc_start: 0.8129 (ppp) cc_final: 0.7839 (ppp) REVERT: A 458 MET cc_start: 0.8780 (tpp) cc_final: 0.8482 (tpp) REVERT: A 543 GLU cc_start: 0.7412 (mp0) cc_final: 0.7052 (mp0) REVERT: A 620 MET cc_start: 0.8801 (tpt) cc_final: 0.8358 (mmm) REVERT: A 847 GLU cc_start: 0.9167 (mp0) cc_final: 0.8966 (mp0) REVERT: A 1389 MET cc_start: 0.9351 (mmm) cc_final: 0.9062 (mmm) REVERT: A 1681 MET cc_start: 0.4855 (mpp) cc_final: 0.4642 (mpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0894 time to fit residues: 11.5935 Evaluate side-chains 70 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 160 optimal weight: 50.0000 chunk 125 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 449 GLN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.066350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047563 restraints weight = 88959.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048979 restraints weight = 51956.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049886 restraints weight = 37003.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050490 restraints weight = 29959.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050776 restraints weight = 26251.971| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15200 Z= 0.131 Angle : 0.579 8.880 21024 Z= 0.300 Chirality : 0.040 0.257 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.343 162.732 3159 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1552 helix: 0.56 (0.19), residues: 732 sheet: -1.05 (0.40), residues: 145 loop : -0.82 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 511 TYR 0.013 0.001 TYR A1624 PHE 0.029 0.001 PHE A1387 TRP 0.014 0.001 TRP A1634 HIS 0.005 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15200) covalent geometry : angle 0.57931 / 0.30 (21024) hydrogen bonds : bond 0.04017 / 2.66 ( 658) hydrogen bonds : angle 4.58829 / 3.18 ( 1802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.75 seconds wall clock time: 38 minutes 36.67 seconds (2316.67 seconds total)