Starting phenix.real_space_refine on Fri May 16 18:55:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yih_39319/05_2025/8yih_39319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yih_39319/05_2025/8yih_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_39319/05_2025/8yih_39319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yih_39319/05_2025/8yih_39319.map" model { file = "/net/cci-nas-00/data/ceres_data/8yih_39319/05_2025/8yih_39319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yih_39319/05_2025/8yih_39319.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.89, per 1000 atoms: 0.54 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: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.70 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: 8.28 Time building geometry restraints manager: 4.07 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=" 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=" C4 ADP A1802 " pdb=" C5 ADP A1802 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C1' U C 46 " pdb=" N1 U C 46 " ideal model delta sigma weight residual 1.470 1.486 -0.016 1.50e-02 4.44e+03 1.16e+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=" CA PRO A 872 " pdb=" CB PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 104.50 95.82 8.68 1.90e+00 2.77e-01 2.09e+01 angle pdb=" CB MET A 344 " pdb=" CG MET A 344 " pdb=" SD MET A 344 " ideal model delta sigma weight residual 112.70 125.02 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB MET A 288 " pdb=" CG MET A 288 " pdb=" SD MET A 288 " ideal model delta sigma weight residual 112.70 124.96 -12.26 3.00e+00 1.11e-01 1.67e+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: 0.990 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.740 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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= 0.143 Angle : 0.643 13.468 21024 Z= 0.326 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 : 18.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (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 TRP 0.020 0.001 TRP A1634 HIS 0.004 0.001 HIS A1522 PHE 0.041 0.001 PHE A 370 TYR 0.010 0.001 TYR A 286 ARG 0.003 0.000 ARG A1658 Details of bonding type rmsd hydrogen bonds : bond 0.15128 ( 658) hydrogen bonds : angle 6.21107 ( 1802) covalent geometry : bond 0.00319 (15200) covalent geometry : angle 0.64331 (21024) *********************** 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 : 1.418 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: 0.2479 time to fit residues: 30.0124 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 : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 407 ASN A 490 GLN A 569 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.066130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047484 restraints weight = 89209.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048943 restraints weight = 50139.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.049904 restraints weight = 34979.864| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15200 Z= 0.189 Angle : 0.627 7.693 21024 Z= 0.319 Chirality : 0.041 0.196 2440 Planarity : 0.005 0.053 2335 Dihedral : 16.374 134.381 3159 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1552 helix: 0.72 (0.19), residues: 724 sheet: -1.26 (0.37), residues: 156 loop : -0.69 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 102 HIS 0.008 0.001 HIS A1305 PHE 0.013 0.002 PHE A 119 TYR 0.017 0.002 TYR A1624 ARG 0.005 0.001 ARG A1448 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 658) hydrogen bonds : angle 4.91395 ( 1802) covalent geometry : bond 0.00405 (15200) covalent geometry : angle 0.62729 (21024) *********************** 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 : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8828 (tpp) cc_final: 0.8607 (tpp) REVERT: A 893 MET cc_start: 0.7954 (tpp) cc_final: 0.7621 (tpp) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2516 time to fit residues: 37.5953 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 : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 62 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** A1270 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.066003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047285 restraints weight = 90295.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048778 restraints weight = 51028.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049771 restraints weight = 35435.094| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15200 Z= 0.163 Angle : 0.588 7.976 21024 Z= 0.299 Chirality : 0.040 0.204 2440 Planarity : 0.004 0.045 2335 Dihedral : 16.280 136.360 3159 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1552 helix: 0.62 (0.19), residues: 736 sheet: -1.22 (0.39), residues: 157 loop : -0.72 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.006 0.001 HIS A1522 PHE 0.010 0.001 PHE A 434 TYR 0.014 0.002 TYR A1624 ARG 0.005 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 658) hydrogen bonds : angle 4.70036 ( 1802) covalent geometry : bond 0.00355 (15200) covalent geometry : angle 0.58767 (21024) *********************** 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 93 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8861 (tpp) cc_final: 0.8602 (tpp) REVERT: A 620 MET cc_start: 0.8837 (tpt) cc_final: 0.8559 (mmm) REVERT: A 862 ASN cc_start: 0.8438 (t0) cc_final: 0.8129 (t0) REVERT: A 893 MET cc_start: 0.8129 (tpp) cc_final: 0.7614 (tpp) REVERT: A 914 ASP cc_start: 0.7656 (t70) cc_final: 0.7230 (m-30) REVERT: A 999 MET cc_start: 0.9154 (ptm) cc_final: 0.8709 (ppp) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2537 time to fit residues: 36.7914 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 : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 0.0980 chunk 121 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 323 HIS ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** 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 = 0.3641 r_free = 0.3641 target = 0.067425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048548 restraints weight = 88552.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050089 restraints weight = 50046.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051078 restraints weight = 34756.567| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15200 Z= 0.111 Angle : 0.552 9.355 21024 Z= 0.278 Chirality : 0.039 0.217 2440 Planarity : 0.004 0.044 2335 Dihedral : 16.110 135.496 3159 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1552 helix: 0.62 (0.19), residues: 738 sheet: -0.85 (0.40), residues: 146 loop : -0.63 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.006 0.001 HIS A 323 PHE 0.011 0.001 PHE A1001 TYR 0.012 0.001 TYR A1624 ARG 0.002 0.000 ARG A 627 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 658) hydrogen bonds : angle 4.47662 ( 1802) covalent geometry : bond 0.00237 (15200) covalent geometry : angle 0.55213 (21024) *********************** 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 104 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8452 (tmm) cc_final: 0.8148 (tmm) REVERT: A 322 MET cc_start: 0.8204 (ppp) cc_final: 0.7908 (ppp) REVERT: A 458 MET cc_start: 0.8813 (tpp) cc_final: 0.8499 (tpp) REVERT: A 543 GLU cc_start: 0.7533 (mp0) cc_final: 0.7192 (mp0) REVERT: A 620 MET cc_start: 0.8758 (tpt) cc_final: 0.8450 (mmm) REVERT: A 625 MET cc_start: 0.8304 (ptp) cc_final: 0.7964 (mtm) REVERT: A 847 GLU cc_start: 0.9147 (mp0) cc_final: 0.8924 (mp0) REVERT: A 893 MET cc_start: 0.7926 (tpp) cc_final: 0.7456 (tpp) REVERT: A 914 ASP cc_start: 0.7736 (t70) cc_final: 0.7305 (m-30) REVERT: A 999 MET cc_start: 0.9019 (ptm) cc_final: 0.8695 (ppp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2373 time to fit residues: 39.2746 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 : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 42 optimal weight: 0.0570 chunk 50 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.068311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049372 restraints weight = 88688.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050922 restraints weight = 50217.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051955 restraints weight = 34817.875| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2498 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= 0.100 Angle : 0.534 7.062 21024 Z= 0.267 Chirality : 0.038 0.199 2440 Planarity : 0.004 0.048 2335 Dihedral : 15.887 134.109 3159 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1552 helix: 0.64 (0.19), residues: 739 sheet: -0.64 (0.41), residues: 141 loop : -0.54 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1634 HIS 0.004 0.001 HIS A1004 PHE 0.011 0.001 PHE A1194 TYR 0.009 0.001 TYR A1624 ARG 0.003 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 658) hydrogen bonds : angle 4.30426 ( 1802) covalent geometry : bond 0.00214 (15200) covalent geometry : angle 0.53390 (21024) *********************** 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 103 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8470 (tmm) cc_final: 0.8156 (tmm) REVERT: A 543 GLU cc_start: 0.7629 (mp0) cc_final: 0.7240 (mp0) REVERT: A 620 MET cc_start: 0.8720 (tpt) cc_final: 0.8291 (mmm) REVERT: A 625 MET cc_start: 0.8386 (ptp) cc_final: 0.8010 (mtm) REVERT: A 768 MET cc_start: 0.8423 (tpp) cc_final: 0.8031 (tpp) REVERT: A 893 MET cc_start: 0.8047 (tpp) cc_final: 0.7534 (tpp) REVERT: A 999 MET cc_start: 0.9069 (ptm) cc_final: 0.8667 (ppp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2376 time to fit residues: 39.3398 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 : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 734 GLN ** 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** ** A1384 GLN ** 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 = 0.3650 r_free = 0.3650 target = 0.067878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048936 restraints weight = 88326.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050503 restraints weight = 49804.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051542 restraints weight = 34258.225| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15200 Z= 0.108 Angle : 0.541 7.243 21024 Z= 0.271 Chirality : 0.038 0.201 2440 Planarity : 0.004 0.047 2335 Dihedral : 15.809 132.093 3159 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1552 helix: 0.66 (0.19), residues: 741 sheet: -0.75 (0.41), residues: 146 loop : -0.53 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1634 HIS 0.004 0.001 HIS A1522 PHE 0.028 0.001 PHE A1387 TYR 0.012 0.001 TYR A 402 ARG 0.003 0.000 ARG A 998 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 658) hydrogen bonds : angle 4.28620 ( 1802) covalent geometry : bond 0.00237 (15200) covalent geometry : angle 0.54140 (21024) *********************** 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 102 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8809 (t70) cc_final: 0.8590 (t0) REVERT: A 543 GLU cc_start: 0.7553 (mp0) cc_final: 0.7198 (mp0) REVERT: A 620 MET cc_start: 0.8692 (tpt) cc_final: 0.8238 (mmm) REVERT: A 625 MET cc_start: 0.8420 (ptp) cc_final: 0.7944 (mtm) REVERT: A 768 MET cc_start: 0.8517 (tpp) cc_final: 0.7880 (tpp) REVERT: A 893 MET cc_start: 0.8046 (tpp) cc_final: 0.7556 (tpp) REVERT: A 999 MET cc_start: 0.9118 (ptm) cc_final: 0.8692 (ppp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2484 time to fit residues: 40.1067 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 : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 122 optimal weight: 0.0470 overall best weight: 2.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 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** ** 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 = 0.3652 r_free = 0.3652 target = 0.067256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048534 restraints weight = 89876.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.049992 restraints weight = 51870.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050957 restraints weight = 36317.134| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15200 Z= 0.129 Angle : 0.562 7.079 21024 Z= 0.284 Chirality : 0.039 0.281 2440 Planarity : 0.004 0.048 2335 Dihedral : 15.805 128.104 3159 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1552 helix: 0.73 (0.19), residues: 738 sheet: -0.79 (0.41), residues: 146 loop : -0.53 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.005 0.001 HIS A1522 PHE 0.022 0.001 PHE A1387 TYR 0.012 0.001 TYR A 402 ARG 0.003 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 658) hydrogen bonds : angle 4.30486 ( 1802) covalent geometry : bond 0.00285 (15200) covalent geometry : angle 0.56213 (21024) *********************** 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 94 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8434 (tmm) cc_final: 0.8030 (tmm) REVERT: A 543 GLU cc_start: 0.7444 (mp0) cc_final: 0.7100 (mp0) REVERT: A 620 MET cc_start: 0.8881 (tpt) cc_final: 0.8427 (mmm) REVERT: A 625 MET cc_start: 0.8476 (ptp) cc_final: 0.8159 (mtm) REVERT: A 768 MET cc_start: 0.8781 (tpp) cc_final: 0.8480 (tpp) REVERT: A 862 ASN cc_start: 0.8399 (t0) cc_final: 0.8055 (t0) REVERT: A 893 MET cc_start: 0.7965 (tpp) cc_final: 0.7464 (tpp) REVERT: A 914 ASP cc_start: 0.7736 (t70) cc_final: 0.7266 (m-30) REVERT: A 922 MET cc_start: 0.8203 (mmp) cc_final: 0.7914 (mmm) REVERT: A 999 MET cc_start: 0.9140 (ptm) cc_final: 0.8681 (ppp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2443 time to fit residues: 36.3448 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 : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 141 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 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** A1286 HIS ** 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 = 0.3584 r_free = 0.3584 target = 0.065193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046334 restraints weight = 89745.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047789 restraints weight = 51058.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.048720 restraints weight = 35720.406| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15200 Z= 0.215 Angle : 0.633 9.013 21024 Z= 0.323 Chirality : 0.040 0.222 2440 Planarity : 0.004 0.046 2335 Dihedral : 16.010 120.740 3159 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1552 helix: 0.67 (0.19), residues: 739 sheet: -0.97 (0.41), residues: 146 loop : -0.70 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.008 0.002 HIS A1522 PHE 0.017 0.002 PHE A1219 TYR 0.016 0.002 TYR A1434 ARG 0.008 0.001 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 658) hydrogen bonds : angle 4.51009 ( 1802) covalent geometry : bond 0.00466 (15200) covalent geometry : angle 0.63348 (21024) *********************** 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 85 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9281 (mmm) cc_final: 0.9009 (mmm) REVERT: A 458 MET cc_start: 0.8366 (tpt) cc_final: 0.7753 (tpt) REVERT: A 543 GLU cc_start: 0.7645 (mp0) cc_final: 0.7384 (mp0) REVERT: A 620 MET cc_start: 0.8962 (tpt) cc_final: 0.8428 (mmm) REVERT: A 625 MET cc_start: 0.8600 (ptp) cc_final: 0.8293 (ptp) REVERT: A 768 MET cc_start: 0.8693 (tpp) cc_final: 0.8328 (tpp) REVERT: A 862 ASN cc_start: 0.8537 (t0) cc_final: 0.8182 (t0) REVERT: A 893 MET cc_start: 0.8031 (tpp) cc_final: 0.7517 (tpp) REVERT: A 999 MET cc_start: 0.9197 (ptm) cc_final: 0.8744 (ppp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2525 time to fit residues: 33.6892 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 : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 108 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 163 optimal weight: 30.0000 chunk 148 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 266 GLN A 695 ASN A 734 GLN A 773 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.064022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.045318 restraints weight = 90734.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046715 restraints weight = 51611.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047636 restraints weight = 36148.037| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15200 Z= 0.223 Angle : 0.668 8.865 21024 Z= 0.341 Chirality : 0.042 0.264 2440 Planarity : 0.005 0.046 2335 Dihedral : 16.315 114.213 3159 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.93 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1552 helix: 0.63 (0.19), residues: 727 sheet: -1.16 (0.41), residues: 145 loop : -0.76 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 102 HIS 0.013 0.002 HIS A1305 PHE 0.023 0.002 PHE A1012 TYR 0.016 0.002 TYR A 402 ARG 0.007 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 658) hydrogen bonds : angle 4.65699 ( 1802) covalent geometry : bond 0.00485 (15200) covalent geometry : angle 0.66800 (21024) *********************** 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 82 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.9415 (ppp) cc_final: 0.9198 (ppp) REVERT: A 543 GLU cc_start: 0.7649 (mp0) cc_final: 0.7294 (mp0) REVERT: A 620 MET cc_start: 0.8968 (tpt) cc_final: 0.8409 (tmm) REVERT: A 625 MET cc_start: 0.8589 (ptp) cc_final: 0.8240 (ptp) REVERT: A 893 MET cc_start: 0.7862 (tpp) cc_final: 0.7383 (tpp) REVERT: A 999 MET cc_start: 0.9193 (ptm) cc_final: 0.8762 (ppp) REVERT: A 1195 LEU cc_start: 0.9443 (tp) cc_final: 0.9238 (tp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2786 time to fit residues: 36.1261 Evaluate side-chains 65 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 55 optimal weight: 0.0470 chunk 102 optimal weight: 4.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 407 ASN A 695 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN ** 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 = 0.3611 r_free = 0.3611 target = 0.065774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047023 restraints weight = 89315.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.048488 restraints weight = 50264.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049440 restraints weight = 34855.676| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15200 Z= 0.132 Angle : 0.589 8.394 21024 Z= 0.297 Chirality : 0.040 0.239 2440 Planarity : 0.004 0.046 2335 Dihedral : 16.127 113.179 3159 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1552 helix: 0.75 (0.19), residues: 727 sheet: -0.95 (0.41), residues: 141 loop : -0.57 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1634 HIS 0.004 0.001 HIS A1004 PHE 0.017 0.001 PHE A1387 TYR 0.013 0.001 TYR A1624 ARG 0.004 0.000 ARG A1418 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 658) hydrogen bonds : angle 4.45533 ( 1802) covalent geometry : bond 0.00293 (15200) covalent geometry : angle 0.58933 (21024) ********************** 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 91 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.9352 (ppp) cc_final: 0.9137 (ppp) REVERT: A 424 MET cc_start: 0.8349 (ppp) cc_final: 0.8026 (ppp) REVERT: A 543 GLU cc_start: 0.7632 (mp0) cc_final: 0.7252 (mp0) REVERT: A 620 MET cc_start: 0.8821 (tpt) cc_final: 0.8321 (tmm) REVERT: A 625 MET cc_start: 0.8593 (ptp) cc_final: 0.8196 (ptp) REVERT: A 893 MET cc_start: 0.7781 (tpp) cc_final: 0.7203 (tpp) REVERT: A 922 MET cc_start: 0.8023 (mmp) cc_final: 0.7819 (mmm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2506 time to fit residues: 36.0663 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 : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 335 HIS ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** 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 = 0.3542 r_free = 0.3542 target = 0.063050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.044683 restraints weight = 90922.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046043 restraints weight = 51633.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.046938 restraints weight = 36026.944| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 15200 Z= 0.295 Angle : 0.740 9.704 21024 Z= 0.378 Chirality : 0.044 0.248 2440 Planarity : 0.005 0.051 2335 Dihedral : 16.358 113.572 3159 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1552 helix: 0.53 (0.19), residues: 717 sheet: -1.40 (0.39), residues: 147 loop : -0.82 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 102 HIS 0.010 0.002 HIS A1522 PHE 0.021 0.002 PHE A1219 TYR 0.019 0.002 TYR A1434 ARG 0.010 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 658) hydrogen bonds : angle 4.90571 ( 1802) covalent geometry : bond 0.00632 (15200) covalent geometry : angle 0.73958 (21024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4145.02 seconds wall clock time: 74 minutes 4.23 seconds (4444.23 seconds total)