Starting phenix.real_space_refine on Fri Jul 3 15:17:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yih_39319/07_2026/8yih_39319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yih_39319/07_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_39319/07_2026/8yih_39319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yih_39319/07_2026/8yih_39319.map" model { file = "/net/cci-nas-00/data/ceres_data/8yih_39319/07_2026/8yih_39319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yih_39319/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.95, per 1000 atoms: 0.20 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: 1.32 Conformation dependent library (CDL) restraints added in 602.8 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: 2.02 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: 3.81 Time building geometry restraints manager: 1.75 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=" 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 bond pdb=" N9 A C 42 " pdb=" C4 A C 42 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.91e+00 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20839 2.69 - 5.39: 156 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: 2110 0.057 - 0.114: 301 0.114 - 0.171: 26 0.171 - 0.228: 2 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=" C2' U C 46 " pdb=" C3' U C 46 " pdb=" O2' U C 46 " pdb=" C1' U C 46 " both_signs ideal model delta sigma weight residual False -2.52 -2.72 0.20 2.00e-01 2.50e+01 1.01e+00 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 2.45 2.27 0.17 2.00e-01 2.50e+01 7.53e-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: 0.950 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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= 0.158 Angle : 0.643 13.468 21024 Z= 0.385 Chirality : 0.039 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 0.00319 / 0.16 (15200) covalent geometry : angle 0.64334 / 0.39 (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 : 0.513 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: 0.1137 time to fit residues: 13.8964 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** ** A 955 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 ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3610 r_free = 0.3610 target = 0.066214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.047482 restraints weight = 90282.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.048966 restraints weight = 50617.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049920 restraints weight = 35215.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050436 restraints weight = 28161.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050871 restraints weight = 24810.360| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1343 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= 0.224 Angle : 0.656 7.949 21024 Z= 0.343 Chirality : 0.042 0.200 2440 Planarity : 0.005 0.065 2335 Dihedral : 16.503 129.546 3159 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.72 % Rotamer: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1552 helix: 0.65 (0.19), residues: 722 sheet: -1.41 (0.36), residues: 167 loop : -0.76 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 627 TYR 0.025 0.002 TYR A 578 PHE 0.016 0.002 PHE A 119 TRP 0.012 0.002 TRP A1634 HIS 0.011 0.002 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (15200) covalent geometry : angle 0.65576 / 0.34 (21024) hydrogen bonds : bond 0.05088 / 3.31 ( 658) hydrogen bonds : angle 5.21371 / 3.62 ( 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 94 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8869 (tpp) cc_final: 0.8655 (tpp) REVERT: A 922 MET cc_start: 0.8093 (mmp) cc_final: 0.7841 (mmm) REVERT: A 1389 MET cc_start: 0.9213 (tpp) cc_final: 0.8880 (mmm) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1084 time to fit residues: 16.1552 Evaluate side-chains 68 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** A1456 HIS ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.067664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.048840 restraints weight = 89372.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050349 restraints weight = 50166.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051371 restraints weight = 34709.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052019 restraints weight = 27548.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052422 restraints weight = 23914.327| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 15200 Z= 0.130 Angle : 0.562 8.676 21024 Z= 0.294 Chirality : 0.040 0.211 2440 Planarity : 0.004 0.050 2335 Dihedral : 16.339 137.266 3159 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -0.31 (0.21), residues: 1552 helix: 0.60 (0.19), residues: 729 sheet: -1.24 (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 998 TYR 0.017 0.002 TYR A1624 PHE 0.010 0.001 PHE A1001 TRP 0.013 0.001 TRP A 102 HIS 0.010 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15200) covalent geometry : angle 0.56224 / 0.29 (21024) hydrogen bonds : bond 0.04302 / 2.83 ( 658) hydrogen bonds : angle 4.80474 / 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 110 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8139 (ppp) cc_final: 0.7857 (ppp) REVERT: A 458 MET cc_start: 0.8876 (tpp) cc_final: 0.8589 (tpp) REVERT: A 543 GLU cc_start: 0.7324 (mp0) cc_final: 0.6976 (mp0) REVERT: A 620 MET cc_start: 0.8675 (tpt) cc_final: 0.8469 (mmm) REVERT: A 625 MET cc_start: 0.8229 (ptp) cc_final: 0.7969 (mtm) REVERT: A 893 MET cc_start: 0.7890 (tpp) cc_final: 0.7599 (tpp) REVERT: A 999 MET cc_start: 0.9062 (ptm) cc_final: 0.8656 (ppp) REVERT: A 1447 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7956 (ttm170) REVERT: A 1479 LEU cc_start: 0.9018 (tp) cc_final: 0.8781 (pp) REVERT: A 1511 THR cc_start: 0.9514 (p) cc_final: 0.9266 (t) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1229 time to fit residues: 20.4743 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 : 0.525 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 0.0010 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 ** 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 = 0.3668 r_free = 0.3668 target = 0.068400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.049488 restraints weight = 89163.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.050967 restraints weight = 51367.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051930 restraints weight = 36097.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052523 restraints weight = 29085.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.052921 restraints weight = 25521.742| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15200 Z= 0.109 Angle : 0.540 8.409 21024 Z= 0.282 Chirality : 0.039 0.214 2440 Planarity : 0.004 0.050 2335 Dihedral : 16.206 141.682 3159 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.00 % 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: -0.26 (0.21), residues: 1552 helix: 0.55 (0.19), residues: 735 sheet: -1.11 (0.37), residues: 167 loop : -0.63 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.014 0.001 TYR A1624 PHE 0.012 0.001 PHE A1012 TRP 0.013 0.001 TRP A 102 HIS 0.008 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15200) covalent geometry : angle 0.54037 / 0.28 (21024) hydrogen bonds : bond 0.03969 / 2.63 ( 658) hydrogen bonds : angle 4.62146 / 3.19 ( 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 105 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8462 (tmm) cc_final: 0.8240 (tmm) REVERT: A 322 MET cc_start: 0.8245 (ppp) cc_final: 0.7966 (ppp) REVERT: A 458 MET cc_start: 0.8776 (tpp) cc_final: 0.8504 (tpp) REVERT: A 543 GLU cc_start: 0.7241 (mp0) cc_final: 0.6881 (mp0) REVERT: A 620 MET cc_start: 0.8691 (tpt) cc_final: 0.8439 (mmm) REVERT: A 625 MET cc_start: 0.8266 (ptp) cc_final: 0.7957 (mtm) REVERT: A 893 MET cc_start: 0.8024 (tpp) cc_final: 0.7600 (tpp) REVERT: A 999 MET cc_start: 0.9028 (ptm) cc_final: 0.8712 (ppp) REVERT: A 1511 THR cc_start: 0.9516 (p) cc_final: 0.9273 (t) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1001 time to fit residues: 17.1003 Evaluate side-chains 79 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 40.0000 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3559 r_free = 0.3559 target = 0.063937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045336 restraints weight = 93310.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.046737 restraints weight = 53432.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047642 restraints weight = 37499.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048215 restraints weight = 30246.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048482 restraints weight = 26556.293| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 15200 Z= 0.360 Angle : 0.786 11.056 21024 Z= 0.407 Chirality : 0.045 0.211 2440 Planarity : 0.006 0.063 2335 Dihedral : 16.405 150.018 3159 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -0.62 (0.21), residues: 1552 helix: 0.34 (0.19), residues: 722 sheet: -1.25 (0.40), residues: 145 loop : -0.95 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 167 TYR 0.024 0.003 TYR A1434 PHE 0.021 0.002 PHE A1219 TRP 0.008 0.002 TRP A1634 HIS 0.014 0.003 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.36 (15200) covalent geometry : angle 0.78630 / 0.41 (21024) hydrogen bonds : bond 0.05450 / 3.51 ( 658) hydrogen bonds : angle 5.14356 / 3.53 ( 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 79 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8814 (tpp) cc_final: 0.8554 (tpp) REVERT: A 620 MET cc_start: 0.8988 (tpt) cc_final: 0.8634 (tmm) REVERT: A 862 ASN cc_start: 0.8407 (t0) cc_final: 0.8063 (t0) REVERT: A 893 MET cc_start: 0.7817 (tpp) cc_final: 0.7380 (tpp) REVERT: A 914 ASP cc_start: 0.7722 (t70) cc_final: 0.7297 (m-30) REVERT: A 1389 MET cc_start: 0.9488 (mmm) cc_final: 0.9018 (mmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1140 time to fit residues: 14.4177 Evaluate side-chains 63 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 0.8980 chunk 125 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** A1267 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.066824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.047904 restraints weight = 88846.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.049357 restraints weight = 51243.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050298 restraints weight = 36149.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050870 restraints weight = 29172.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051226 restraints weight = 25651.139| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15200 Z= 0.130 Angle : 0.568 7.986 21024 Z= 0.298 Chirality : 0.040 0.214 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.401 154.049 3159 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.55 (0.19), residues: 725 sheet: -1.27 (0.38), residues: 157 loop : -0.72 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 998 TYR 0.015 0.002 TYR A1624 PHE 0.011 0.001 PHE A1001 TRP 0.012 0.001 TRP A1634 HIS 0.006 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15200) covalent geometry : angle 0.56837 / 0.30 (21024) hydrogen bonds : bond 0.04119 / 2.72 ( 658) hydrogen bonds : angle 4.66077 / 3.22 ( 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 92 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8518 (tmm) cc_final: 0.8237 (tmm) REVERT: A 322 MET cc_start: 0.8220 (ppp) cc_final: 0.7894 (ppp) REVERT: A 458 MET cc_start: 0.8854 (tpp) cc_final: 0.8558 (tpp) REVERT: A 543 GLU cc_start: 0.7374 (mp0) cc_final: 0.7015 (mp0) REVERT: A 620 MET cc_start: 0.8780 (tpt) cc_final: 0.8439 (mmm) REVERT: A 862 ASN cc_start: 0.8342 (t0) cc_final: 0.7984 (t0) REVERT: A 893 MET cc_start: 0.8017 (tpp) cc_final: 0.7557 (tpp) REVERT: A 914 ASP cc_start: 0.7674 (t70) cc_final: 0.7229 (m-30) REVERT: A 1029 MET cc_start: 0.8660 (ttm) cc_final: 0.8359 (ttm) REVERT: A 1389 MET cc_start: 0.9390 (mmm) cc_final: 0.9131 (mmm) REVERT: A 1511 THR cc_start: 0.9520 (p) cc_final: 0.9278 (t) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1069 time to fit residues: 16.0262 Evaluate side-chains 72 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 9.9990 chunk 63 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 162 optimal weight: 40.0000 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN ** 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** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.065840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.047083 restraints weight = 89821.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048492 restraints weight = 51883.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049405 restraints weight = 36742.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049977 restraints weight = 29746.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.050312 restraints weight = 26193.342| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15200 Z= 0.187 Angle : 0.608 9.618 21024 Z= 0.316 Chirality : 0.041 0.237 2440 Planarity : 0.005 0.051 2335 Dihedral : 16.394 158.888 3159 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.33 (0.21), residues: 1552 helix: 0.59 (0.19), residues: 726 sheet: -1.08 (0.40), residues: 145 loop : -0.81 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 998 TYR 0.015 0.002 TYR A1624 PHE 0.012 0.001 PHE A1219 TRP 0.012 0.001 TRP A1634 HIS 0.008 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (15200) covalent geometry : angle 0.60794 / 0.32 (21024) hydrogen bonds : bond 0.04366 / 2.87 ( 658) hydrogen bonds : angle 4.68265 / 3.22 ( 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 88 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8477 (tmm) cc_final: 0.8170 (tmm) REVERT: A 322 MET cc_start: 0.8296 (ppp) cc_final: 0.7991 (ppp) REVERT: A 458 MET cc_start: 0.8839 (tpp) cc_final: 0.8559 (tpp) REVERT: A 620 MET cc_start: 0.8900 (tpt) cc_final: 0.8518 (mmm) REVERT: A 862 ASN cc_start: 0.8330 (t0) cc_final: 0.7957 (t0) REVERT: A 893 MET cc_start: 0.8075 (tpp) cc_final: 0.7625 (tpp) REVERT: A 914 ASP cc_start: 0.7385 (t70) cc_final: 0.6991 (m-30) REVERT: A 1029 MET cc_start: 0.8636 (ttm) cc_final: 0.8374 (ttm) REVERT: A 1389 MET cc_start: 0.9372 (mmm) cc_final: 0.9138 (mmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1028 time to fit residues: 14.6244 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 : 0.347 ------------------------------------------------------------------------------- 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: 9.9990 chunk 101 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN ** 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** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.065190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046412 restraints weight = 91641.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.047811 restraints weight = 53157.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.048728 restraints weight = 37768.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049286 restraints weight = 30563.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049581 restraints weight = 26923.929| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2502 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= 0.225 Angle : 0.638 9.220 21024 Z= 0.333 Chirality : 0.042 0.223 2440 Planarity : 0.005 0.050 2335 Dihedral : 16.465 162.584 3159 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.45 (0.21), residues: 1552 helix: 0.49 (0.19), residues: 725 sheet: -1.14 (0.40), residues: 145 loop : -0.88 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 866 TYR 0.015 0.002 TYR A1624 PHE 0.031 0.002 PHE A1387 TRP 0.011 0.001 TRP A 102 HIS 0.009 0.002 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (15200) covalent geometry : angle 0.63793 / 0.33 (21024) hydrogen bonds : bond 0.04488 / 2.93 ( 658) hydrogen bonds : angle 4.79735 / 3.31 ( 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 84 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8110 (ppp) cc_final: 0.7809 (ppp) REVERT: A 458 MET cc_start: 0.8824 (tpp) cc_final: 0.8543 (tpp) REVERT: A 620 MET cc_start: 0.8944 (tpt) cc_final: 0.8506 (mmm) REVERT: A 768 MET cc_start: 0.8315 (tpp) cc_final: 0.7925 (tpp) REVERT: A 862 ASN cc_start: 0.8478 (t0) cc_final: 0.8104 (t0) REVERT: A 893 MET cc_start: 0.8066 (tpp) cc_final: 0.7744 (tpp) REVERT: A 922 MET cc_start: 0.8218 (mmp) cc_final: 0.7912 (mmm) REVERT: A 1029 MET cc_start: 0.8641 (ttm) cc_final: 0.8345 (ttm) REVERT: A 1389 MET cc_start: 0.9354 (mmm) cc_final: 0.9116 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0998 time to fit residues: 13.3533 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 : 0.544 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 407 ASN A 449 GLN A 516 GLN A 517 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** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.066498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048454 restraints weight = 88633.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049752 restraints weight = 49114.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.050710 restraints weight = 31742.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050774 restraints weight = 28800.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050891 restraints weight = 24717.787| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2579 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= 0.117 Angle : 0.571 8.641 21024 Z= 0.296 Chirality : 0.040 0.250 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.405 164.871 3159 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 0.07 % Allowed : 1.00 % Favored : 98.93 % 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: -0.26 (0.21), residues: 1552 helix: 0.58 (0.19), residues: 733 sheet: -0.94 (0.40), residues: 145 loop : -0.73 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.014 0.002 TYR A1037 PHE 0.030 0.001 PHE A1387 TRP 0.014 0.001 TRP A1634 HIS 0.006 0.001 HIS A 778 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15200) covalent geometry : angle 0.57096 / 0.30 (21024) hydrogen bonds : bond 0.03973 / 2.63 ( 658) hydrogen bonds : angle 4.55531 / 3.15 ( 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 93 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8488 (tmm) cc_final: 0.8200 (tmm) REVERT: A 322 MET cc_start: 0.8021 (ppp) cc_final: 0.7706 (ppp) REVERT: A 458 MET cc_start: 0.8810 (tpp) cc_final: 0.8523 (tpp) REVERT: A 543 GLU cc_start: 0.7517 (mp0) cc_final: 0.7153 (mp0) REVERT: A 620 MET cc_start: 0.8728 (tpt) cc_final: 0.8277 (mmm) REVERT: A 847 GLU cc_start: 0.9178 (mp0) cc_final: 0.8933 (mp0) REVERT: A 862 ASN cc_start: 0.8490 (t0) cc_final: 0.8126 (t0) REVERT: A 893 MET cc_start: 0.7922 (tpp) cc_final: 0.7431 (tpp) REVERT: A 1511 THR cc_start: 0.9527 (p) cc_final: 0.9293 (t) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1037 time to fit residues: 15.5597 Evaluate side-chains 74 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 105 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 516 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** ** 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 = 0.3615 r_free = 0.3615 target = 0.066182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047357 restraints weight = 90198.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.048795 restraints weight = 52117.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.049700 restraints weight = 36919.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050302 restraints weight = 29891.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050667 restraints weight = 26222.649| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2649 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= 0.157 Angle : 0.589 8.264 21024 Z= 0.306 Chirality : 0.041 0.220 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.373 167.922 3159 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % 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: -0.33 (0.21), residues: 1552 helix: 0.56 (0.19), residues: 732 sheet: -0.93 (0.41), residues: 145 loop : -0.84 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 627 TYR 0.014 0.001 TYR A1624 PHE 0.027 0.001 PHE A1387 TRP 0.013 0.001 TRP A1634 HIS 0.007 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (15200) covalent geometry : angle 0.58852 / 0.31 (21024) hydrogen bonds : bond 0.04064 / 2.66 ( 658) hydrogen bonds : angle 4.58520 / 3.16 ( 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 87 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8486 (tmm) cc_final: 0.8198 (tmm) REVERT: A 322 MET cc_start: 0.8088 (ppp) cc_final: 0.7794 (ppp) REVERT: A 458 MET cc_start: 0.8775 (tpp) cc_final: 0.8473 (tpp) REVERT: A 543 GLU cc_start: 0.7379 (mp0) cc_final: 0.7020 (mp0) REVERT: A 620 MET cc_start: 0.8807 (tpt) cc_final: 0.8378 (mmm) REVERT: A 768 MET cc_start: 0.8344 (tpp) cc_final: 0.8099 (tpp) REVERT: A 862 ASN cc_start: 0.8499 (t0) cc_final: 0.8124 (t0) REVERT: A 893 MET cc_start: 0.7966 (tpp) cc_final: 0.7507 (tpp) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.0981 time to fit residues: 13.8822 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 : 0.492 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 160 optimal weight: 30.0000 chunk 125 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 516 GLN A 695 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** 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 = 0.3623 r_free = 0.3623 target = 0.066682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047791 restraints weight = 88527.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049291 restraints weight = 50169.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.050286 restraints weight = 34975.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050887 restraints weight = 27866.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051273 restraints weight = 24371.616| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15200 Z= 0.115 Angle : 0.563 8.398 21024 Z= 0.292 Chirality : 0.040 0.238 2440 Planarity : 0.004 0.056 2335 Dihedral : 16.317 170.525 3159 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % 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: -0.25 (0.21), residues: 1552 helix: 0.58 (0.19), residues: 732 sheet: -0.81 (0.41), residues: 146 loop : -0.76 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 627 TYR 0.012 0.001 TYR A1000 PHE 0.028 0.001 PHE A1387 TRP 0.015 0.001 TRP A1634 HIS 0.004 0.001 HIS A 778 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15200) covalent geometry : angle 0.56334 / 0.29 (21024) hydrogen bonds : bond 0.03808 / 2.51 ( 658) hydrogen bonds : angle 4.46416 / 3.08 ( 1802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.04 seconds wall clock time: 41 minutes 6.83 seconds (2466.83 seconds total)