Starting phenix.real_space_refine on Fri Jun 13 06:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yih_39319/06_2025/8yih_39319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yih_39319/06_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_39319/06_2025/8yih_39319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yih_39319/06_2025/8yih_39319.map" model { file = "/net/cci-nas-00/data/ceres_data/8yih_39319/06_2025/8yih_39319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yih_39319/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.99, per 1000 atoms: 0.61 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: 4.24 Conformation dependent library (CDL) restraints added in 1.8 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: 6.25 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: 8.89 Time building geometry restraints manager: 4.97 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: 0.970 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 44.820 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- 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 : 1.618 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: 0.2674 time to fit residues: 32.5190 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 : 1.596 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047481 restraints weight = 89209.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048955 restraints weight = 50168.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.049882 restraints weight = 34865.309| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8826 (tpp) cc_final: 0.8603 (tpp) REVERT: A 893 MET cc_start: 0.7956 (tpp) cc_final: 0.7621 (tpp) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2577 time to fit residues: 38.4034 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 : 1.684 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.065112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.046506 restraints weight = 90903.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047976 restraints weight = 51302.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048926 restraints weight = 35673.101| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15200 Z= 0.205 Angle : 0.629 9.285 21024 Z= 0.321 Chirality : 0.041 0.205 2440 Planarity : 0.005 0.050 2335 Dihedral : 16.375 136.403 3159 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.52 % Rotamer: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.21), residues: 1552 helix: 0.62 (0.19), residues: 724 sheet: -1.27 (0.38), residues: 156 loop : -0.76 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.008 0.002 HIS A1522 PHE 0.011 0.002 PHE A1219 TYR 0.015 0.002 TYR A1624 ARG 0.007 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 658) hydrogen bonds : angle 4.82564 ( 1802) covalent geometry : bond 0.00443 (15200) covalent geometry : angle 0.62888 (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 86 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8883 (tpp) cc_final: 0.8631 (tpp) REVERT: A 620 MET cc_start: 0.8893 (tpt) cc_final: 0.8610 (mmm) REVERT: A 862 ASN cc_start: 0.8426 (t0) cc_final: 0.8125 (t0) REVERT: A 893 MET cc_start: 0.8130 (tpp) cc_final: 0.7499 (tpp) REVERT: A 914 ASP cc_start: 0.7783 (t70) cc_final: 0.7311 (m-30) REVERT: A 999 MET cc_start: 0.9184 (ptm) cc_final: 0.8695 (ppp) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2738 time to fit residues: 36.5117 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 : 1.448 ------------------------------------------------------------------------------- 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: 3.9990 chunk 121 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** A1270 GLN ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.065793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047067 restraints weight = 89028.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048574 restraints weight = 49946.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.049557 restraints weight = 34521.725| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15200 Z= 0.154 Angle : 0.588 10.787 21024 Z= 0.298 Chirality : 0.040 0.207 2440 Planarity : 0.004 0.044 2335 Dihedral : 16.301 135.464 3159 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % 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: -0.21 (0.22), residues: 1552 helix: 0.62 (0.19), residues: 732 sheet: -1.03 (0.40), residues: 145 loop : -0.68 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.007 0.001 HIS A 323 PHE 0.012 0.001 PHE A1001 TYR 0.014 0.001 TYR A1624 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 658) hydrogen bonds : angle 4.62880 ( 1802) covalent geometry : bond 0.00338 (15200) covalent geometry : angle 0.58755 (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 92 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8489 (tmm) cc_final: 0.8158 (tmm) REVERT: A 322 MET cc_start: 0.8158 (ppp) cc_final: 0.7870 (ppp) REVERT: A 458 MET cc_start: 0.8854 (tpp) cc_final: 0.8568 (tpp) REVERT: A 543 GLU cc_start: 0.7490 (mp0) cc_final: 0.7138 (mp0) REVERT: A 620 MET cc_start: 0.8775 (tpt) cc_final: 0.8442 (mmm) REVERT: A 862 ASN cc_start: 0.8471 (t0) cc_final: 0.8155 (t0) REVERT: A 893 MET cc_start: 0.8044 (tpp) cc_final: 0.7568 (tpp) REVERT: A 914 ASP cc_start: 0.7724 (t70) cc_final: 0.7237 (m-30) REVERT: A 999 MET cc_start: 0.9094 (ptm) cc_final: 0.8708 (ppp) REVERT: A 1195 LEU cc_start: 0.9355 (tp) cc_final: 0.9153 (tp) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.2523 time to fit residues: 37.2369 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 : 1.617 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.0040 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- 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 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.066532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.047778 restraints weight = 89423.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049297 restraints weight = 50519.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050284 restraints weight = 35053.086| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15200 Z= 0.126 Angle : 0.554 7.130 21024 Z= 0.279 Chirality : 0.039 0.200 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.162 133.322 3159 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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 (0.22), residues: 1552 helix: 0.63 (0.19), residues: 740 sheet: -0.96 (0.40), residues: 146 loop : -0.66 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1634 HIS 0.004 0.001 HIS A1522 PHE 0.023 0.001 PHE A1387 TYR 0.012 0.001 TYR A1624 ARG 0.006 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 658) hydrogen bonds : angle 4.48869 ( 1802) covalent geometry : bond 0.00277 (15200) covalent geometry : angle 0.55390 (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 94 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8227 (ppp) cc_final: 0.7923 (ppp) REVERT: A 458 MET cc_start: 0.8820 (tpp) cc_final: 0.8511 (tpp) REVERT: A 543 GLU cc_start: 0.7636 (mp0) cc_final: 0.7280 (mp0) REVERT: A 620 MET cc_start: 0.8662 (tpt) cc_final: 0.8209 (mmm) REVERT: A 862 ASN cc_start: 0.8456 (t0) cc_final: 0.8113 (t0) REVERT: A 893 MET cc_start: 0.8028 (tpp) cc_final: 0.7518 (tpp) REVERT: A 914 ASP cc_start: 0.7688 (t70) cc_final: 0.7200 (m-30) REVERT: A 922 MET cc_start: 0.8171 (mmp) cc_final: 0.7921 (mmm) REVERT: A 999 MET cc_start: 0.9092 (ptm) cc_final: 0.8655 (ppp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2489 time to fit residues: 37.3962 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 : 1.568 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 122 optimal weight: 0.0270 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- 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** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.067507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.048400 restraints weight = 89636.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049916 restraints weight = 51046.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.050916 restraints weight = 35671.273| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15200 Z= 0.108 Angle : 0.549 7.485 21024 Z= 0.276 Chirality : 0.039 0.199 2440 Planarity : 0.004 0.048 2335 Dihedral : 15.994 129.407 3159 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % 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: -0.13 (0.21), residues: 1552 helix: 0.65 (0.19), residues: 741 sheet: -0.91 (0.40), residues: 146 loop : -0.63 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.005 0.001 HIS A1004 PHE 0.023 0.001 PHE A1387 TYR 0.010 0.001 TYR A1624 ARG 0.004 0.000 ARG A 627 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 658) hydrogen bonds : angle 4.39375 ( 1802) covalent geometry : bond 0.00235 (15200) covalent geometry : angle 0.54919 (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 96 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8543 (tmm) cc_final: 0.8092 (tmm) REVERT: A 458 MET cc_start: 0.8788 (tpp) cc_final: 0.8484 (tpp) REVERT: A 543 GLU cc_start: 0.7608 (mp0) cc_final: 0.7248 (mp0) REVERT: A 620 MET cc_start: 0.8673 (tpt) cc_final: 0.8180 (tmm) REVERT: A 862 ASN cc_start: 0.8511 (t0) cc_final: 0.8179 (t0) REVERT: A 893 MET cc_start: 0.7977 (tpp) cc_final: 0.7457 (tpp) REVERT: A 999 MET cc_start: 0.9070 (ptm) cc_final: 0.8724 (ppp) REVERT: A 1195 LEU cc_start: 0.9364 (tp) cc_final: 0.9163 (tp) REVERT: A 1205 ASP cc_start: 0.8486 (m-30) cc_final: 0.8285 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2885 time to fit residues: 45.1141 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 : 1.474 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.064991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046203 restraints weight = 91915.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.047677 restraints weight = 51984.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048628 restraints weight = 36240.089| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15200 Z= 0.212 Angle : 0.633 9.130 21024 Z= 0.323 Chirality : 0.040 0.215 2440 Planarity : 0.004 0.048 2335 Dihedral : 16.166 123.840 3159 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -0.21 (0.21), residues: 1552 helix: 0.66 (0.19), residues: 734 sheet: -1.08 (0.40), residues: 146 loop : -0.72 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.010 0.002 HIS A1305 PHE 0.016 0.002 PHE A1387 TYR 0.016 0.002 TYR A1434 ARG 0.006 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 658) hydrogen bonds : angle 4.57635 ( 1802) covalent geometry : bond 0.00459 (15200) covalent geometry : angle 0.63321 (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 83 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8798 (tpp) cc_final: 0.8515 (tpp) REVERT: A 543 GLU cc_start: 0.7685 (mp0) cc_final: 0.7432 (mp0) REVERT: A 620 MET cc_start: 0.8921 (tpt) cc_final: 0.8326 (tmm) REVERT: A 768 MET cc_start: 0.8637 (tpp) cc_final: 0.7946 (tpp) REVERT: A 893 MET cc_start: 0.7973 (tpp) cc_final: 0.7457 (tpp) REVERT: A 999 MET cc_start: 0.9204 (ptm) cc_final: 0.8769 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2714 time to fit residues: 35.3849 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 : 1.643 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 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** A1329 ASN ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.063700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.044992 restraints weight = 92542.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.046386 restraints weight = 52659.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047295 restraints weight = 37085.321| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 15200 Z= 0.252 Angle : 0.698 9.283 21024 Z= 0.354 Chirality : 0.042 0.233 2440 Planarity : 0.005 0.051 2335 Dihedral : 16.413 113.770 3159 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -0.48 (0.21), residues: 1552 helix: 0.53 (0.19), residues: 728 sheet: -1.42 (0.39), residues: 145 loop : -0.91 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 102 HIS 0.009 0.002 HIS A1004 PHE 0.017 0.002 PHE A 423 TYR 0.017 0.002 TYR A1434 ARG 0.008 0.001 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 658) hydrogen bonds : angle 4.82839 ( 1802) covalent geometry : bond 0.00543 (15200) covalent geometry : angle 0.69785 (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 78 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8621 (tmm) cc_final: 0.8064 (tmm) REVERT: A 458 MET cc_start: 0.8813 (tpp) cc_final: 0.8541 (tpp) REVERT: A 543 GLU cc_start: 0.7748 (mp0) cc_final: 0.7493 (mp0) REVERT: A 620 MET cc_start: 0.8967 (tpt) cc_final: 0.8364 (tmm) REVERT: A 768 MET cc_start: 0.8574 (tpp) cc_final: 0.8228 (tpp) REVERT: A 922 MET cc_start: 0.8052 (mmp) cc_final: 0.7846 (mmm) REVERT: A 999 MET cc_start: 0.9239 (ptm) cc_final: 0.8895 (ppp) REVERT: A 1389 MET cc_start: 0.9493 (mmm) cc_final: 0.9181 (mmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2866 time to fit residues: 35.9731 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 : 1.950 ------------------------------------------------------------------------------- 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: 4.9990 chunk 160 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 163 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.064845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046036 restraints weight = 90707.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.047449 restraints weight = 51235.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048392 restraints weight = 35978.947| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15200 Z= 0.164 Angle : 0.609 8.304 21024 Z= 0.309 Chirality : 0.040 0.213 2440 Planarity : 0.004 0.048 2335 Dihedral : 16.315 112.606 3159 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.32 (0.21), residues: 1552 helix: 0.68 (0.19), residues: 726 sheet: -1.37 (0.39), residues: 145 loop : -0.84 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1634 HIS 0.006 0.001 HIS A1522 PHE 0.014 0.001 PHE A 423 TYR 0.014 0.002 TYR A1624 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 658) hydrogen bonds : angle 4.62334 ( 1802) covalent geometry : bond 0.00361 (15200) covalent geometry : angle 0.60946 (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 86 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8832 (tpp) cc_final: 0.8539 (tpp) REVERT: A 543 GLU cc_start: 0.7669 (mp0) cc_final: 0.7314 (mp0) REVERT: A 620 MET cc_start: 0.8828 (tpt) cc_final: 0.8264 (tmm) REVERT: A 768 MET cc_start: 0.8673 (tpp) cc_final: 0.8225 (tpp) REVERT: A 893 MET cc_start: 0.7680 (tpp) cc_final: 0.7070 (tpp) REVERT: A 922 MET cc_start: 0.8073 (mmp) cc_final: 0.7850 (mmm) REVERT: A 999 MET cc_start: 0.9203 (ptm) cc_final: 0.8757 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2633 time to fit residues: 35.8219 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 : 1.627 ------------------------------------------------------------------------------- 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: 10.0000 chunk 57 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.066788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047802 restraints weight = 90099.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049308 restraints weight = 50688.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050300 restraints weight = 35222.735| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3315 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 : 0.570 7.381 21024 Z= 0.285 Chirality : 0.039 0.222 2440 Planarity : 0.004 0.048 2335 Dihedral : 16.068 112.569 3159 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.17 % 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: -0.14 (0.21), residues: 1552 helix: 0.74 (0.19), residues: 726 sheet: -1.13 (0.40), residues: 146 loop : -0.67 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1634 HIS 0.004 0.001 HIS A1004 PHE 0.017 0.001 PHE A1387 TYR 0.013 0.001 TYR A1000 ARG 0.006 0.000 ARG A 928 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 658) hydrogen bonds : angle 4.43164 ( 1802) covalent geometry : bond 0.00240 (15200) covalent geometry : angle 0.56952 (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 90 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8790 (tpp) cc_final: 0.8492 (tpp) REVERT: A 543 GLU cc_start: 0.7683 (mp0) cc_final: 0.7400 (mp0) REVERT: A 620 MET cc_start: 0.8735 (tpt) cc_final: 0.8191 (tmm) REVERT: A 768 MET cc_start: 0.8764 (tpp) cc_final: 0.8009 (tpp) REVERT: A 893 MET cc_start: 0.7739 (tpp) cc_final: 0.7109 (tpp) REVERT: A 922 MET cc_start: 0.8072 (mmp) cc_final: 0.7848 (mmm) REVERT: A 999 MET cc_start: 0.9129 (ptm) cc_final: 0.8641 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2427 time to fit residues: 35.2461 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 : 1.446 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.064400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045689 restraints weight = 91377.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.047099 restraints weight = 51959.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048020 restraints weight = 36345.615| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15200 Z= 0.205 Angle : 0.644 8.181 21024 Z= 0.327 Chirality : 0.041 0.205 2440 Planarity : 0.004 0.049 2335 Dihedral : 16.190 113.540 3159 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % 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: -0.26 (0.21), residues: 1552 helix: 0.71 (0.19), residues: 725 sheet: -1.33 (0.39), residues: 147 loop : -0.77 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 102 HIS 0.009 0.001 HIS A1522 PHE 0.018 0.002 PHE A1194 TYR 0.017 0.002 TYR A 402 ARG 0.006 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 658) hydrogen bonds : angle 4.63681 ( 1802) covalent geometry : bond 0.00449 (15200) covalent geometry : angle 0.64359 (21024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4554.19 seconds wall clock time: 81 minutes 53.81 seconds (4913.81 seconds total)