Starting phenix.real_space_refine on Fri Jul 3 05:46:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6t_49074/07_2026/9n6t_49074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6t_49074/07_2026/9n6t_49074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6t_49074/07_2026/9n6t_49074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6t_49074/07_2026/9n6t_49074.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6t_49074/07_2026/9n6t_49074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6t_49074/07_2026/9n6t_49074.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 125 5.49 5 S 22 5.16 5 C 7186 2.51 5 N 2090 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12003 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1846 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 39, 'rna3p_pyr': 36} Link IDs: {'rna2p': 11, 'rna3p': 75} Chain: "A" Number of atoms: 9379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9379 Classifications: {'peptide': 1134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1103} Chain breaks: 6 Time building chain proxies: 2.35, per 1000 atoms: 0.20 Number of scatterers: 12003 At special positions: 0 Unit cell: (76.506, 109.161, 143.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 125 15.00 O 2580 8.00 N 2090 7.00 C 7186 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: 0.98 Conformation dependent library (CDL) restraints added in 398.7 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 51.1% alpha, 13.2% beta 44 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 51 through 81 removed outlier: 3.716A pdb=" N LYS A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.743A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 removed outlier: 4.201A pdb=" N LYS A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.055A pdb=" N TRP A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.865A pdb=" N THR A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.541A pdb=" N PHE A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.613A pdb=" N ILE A 445 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 473 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.715A pdb=" N SER A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 551 through 564 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 605 through 622 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 858 through 886 removed outlier: 5.103A pdb=" N GLN A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 880 " --> pdb=" O ASN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 911 Proline residue: A 905 - end of helix Processing helix chain 'A' and resid 916 through 924 Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 1088 through 1109 Processing helix chain 'A' and resid 1112 through 1114 No H-bonds generated for 'chain 'A' and resid 1112 through 1114' Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.513A pdb=" N GLY A1129 " --> pdb=" O ILE A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1141 Processing helix chain 'A' and resid 1143 through 1148 removed outlier: 3.575A pdb=" N GLN A1147 " --> pdb=" O ASP A1143 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1143 through 1148' Processing helix chain 'A' and resid 1157 through 1176 removed outlier: 4.158A pdb=" N HIS A1161 " --> pdb=" O ALA A1157 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A1162 " --> pdb=" O SER A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1212 Processing helix chain 'A' and resid 1281 through 1292 removed outlier: 3.985A pdb=" N LEU A1292 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1295 No H-bonds generated for 'chain 'A' and resid 1293 through 1295' Processing helix chain 'A' and resid 1307 through 1318 removed outlier: 3.671A pdb=" N LEU A1311 " --> pdb=" O THR A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1345 removed outlier: 3.751A pdb=" N ASN A1345 " --> pdb=" O ILE A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1349 Processing helix chain 'A' and resid 1354 through 1362 Processing helix chain 'A' and resid 1374 through 1384 removed outlier: 3.553A pdb=" N VAL A1378 " --> pdb=" O SER A1374 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A1384 " --> pdb=" O GLN A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1387 No H-bonds generated for 'chain 'A' and resid 1385 through 1387' Processing helix chain 'A' and resid 1397 through 1411 Processing helix chain 'A' and resid 1415 through 1424 Processing helix chain 'A' and resid 1429 through 1433 removed outlier: 3.974A pdb=" N LEU A1432 " --> pdb=" O ILE A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1475 removed outlier: 3.831A pdb=" N ASP A1475 " --> pdb=" O SER A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1542 Processing helix chain 'A' and resid 1568 through 1578 Processing helix chain 'A' and resid 1585 through 1594 removed outlier: 4.003A pdb=" N LYS A1594 " --> pdb=" O LEU A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1628 removed outlier: 3.714A pdb=" N GLY A1620 " --> pdb=" O MET A1616 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A1621 " --> pdb=" O LYS A1617 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A1624 " --> pdb=" O GLY A1620 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.525A pdb=" N ASP A1119 " --> pdb=" O ILE A 892 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 9.370A pdb=" N SER A1219 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 37 " --> pdb=" O SER A1219 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LYS A1221 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 39 " --> pdb=" O LYS A1221 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A1223 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU A 41 " --> pdb=" O LEU A1223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA5, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA6, first strand: chain 'A' and resid 629 through 633 removed outlier: 7.409A pdb=" N GLU A 630 " --> pdb=" O THR A 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA8, first strand: chain 'A' and resid 1440 through 1446 removed outlier: 4.566A pdb=" N PHE A1440 " --> pdb=" O ILE A1372 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1442 " --> pdb=" O VAL A1370 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG A1366 " --> pdb=" O THR A1446 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG A1369 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N ILE A1243 " --> pdb=" O ARG A1369 " (cutoff:3.500A) removed outlier: 13.917A pdb=" N LYS A1371 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 18.089A pdb=" N ASP A1241 " --> pdb=" O LYS A1371 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY A1242 " --> pdb=" O ASN A1468 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN A1468 " --> pdb=" O GLY A1242 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A1466 " --> pdb=" O TYR A1244 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU A1246 " --> pdb=" O TYR A1464 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N TYR A1464 " --> pdb=" O GLU A1246 " (cutoff:3.500A) removed outlier: 17.945A pdb=" N TYR A1248 " --> pdb=" O PHE A1462 " (cutoff:3.500A) removed outlier: 22.567A pdb=" N PHE A1462 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1269 through 1272 removed outlier: 4.329A pdb=" N VAL A1260 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1275 through 1276 Processing sheet with id=AB2, first strand: chain 'A' and resid 1389 through 1390 Processing sheet with id=AB3, first strand: chain 'A' and resid 1490 through 1495 Processing sheet with id=AB4, first strand: chain 'A' and resid 1530 through 1532 removed outlier: 4.194A pdb=" N ILE A1546 " --> pdb=" O VAL A1532 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A1561 " --> pdb=" O ALA A1544 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A1546 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG A1559 " --> pdb=" O ILE A1546 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR A1548 " --> pdb=" O LYS A1557 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A1557 " --> pdb=" O TYR A1548 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2526 1.33 - 1.45: 3431 1.45 - 1.58: 6256 1.58 - 1.70: 249 1.70 - 1.82: 33 Bond restraints: 12495 Sorted by residual: bond pdb=" C3' DT B 43 " pdb=" C2' DT B 43 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DT B 39 " pdb=" C2' DT B 39 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" N1 U D 70 " pdb=" C2 U D 70 " ideal model delta sigma weight residual 1.381 1.411 -0.030 9.00e-03 1.23e+04 1.13e+01 bond pdb=" C3' DT B 40 " pdb=" C2' DT B 40 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DC B 60 " pdb=" C2' DC B 60 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.29e+00 ... (remaining 12490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 17068 2.90 - 5.80: 296 5.80 - 8.71: 40 8.71 - 11.61: 4 11.61 - 14.51: 5 Bond angle restraints: 17413 Sorted by residual: angle pdb=" N1 U D 70 " pdb=" C2 U D 70 " pdb=" O2 U D 70 " ideal model delta sigma weight residual 122.80 129.63 -6.83 7.00e-01 2.04e+00 9.53e+01 angle pdb=" C1' U D 70 " pdb=" N1 U D 70 " pdb=" C2 U D 70 " ideal model delta sigma weight residual 117.70 129.32 -11.62 1.20e+00 6.94e-01 9.37e+01 angle pdb=" O2 U D 70 " pdb=" C2 U D 70 " pdb=" N3 U D 70 " ideal model delta sigma weight residual 122.20 115.64 6.56 7.00e-01 2.04e+00 8.77e+01 angle pdb=" O4' DG C 30 " pdb=" C1' DG C 30 " pdb=" N9 DG C 30 " ideal model delta sigma weight residual 108.00 112.97 -4.97 7.00e-01 2.04e+00 5.04e+01 angle pdb=" C1' U D 70 " pdb=" N1 U D 70 " pdb=" C6 U D 70 " ideal model delta sigma weight residual 121.20 112.58 8.62 1.40e+00 5.10e-01 3.79e+01 ... (remaining 17408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.36: 6926 25.36 - 50.72: 495 50.72 - 76.08: 174 76.08 - 101.45: 12 101.45 - 126.81: 3 Dihedral angle restraints: 7610 sinusoidal: 4243 harmonic: 3367 Sorted by residual: dihedral pdb=" O4' U D 71 " pdb=" C1' U D 71 " pdb=" N1 U D 71 " pdb=" C2 U D 71 " ideal model delta sinusoidal sigma weight residual 200.00 73.19 126.81 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' U D 70 " pdb=" C1' U D 70 " pdb=" N1 U D 70 " pdb=" C2 U D 70 " ideal model delta sinusoidal sigma weight residual 232.00 137.19 94.81 1 1.70e+01 3.46e-03 3.60e+01 dihedral pdb=" CA LYS A 639 " pdb=" C LYS A 639 " pdb=" N TYR A 640 " pdb=" CA TYR A 640 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1489 0.061 - 0.122: 392 0.122 - 0.183: 72 0.183 - 0.244: 21 0.244 - 0.305: 3 Chirality restraints: 1977 Sorted by residual: chirality pdb=" CA ASN A 451 " pdb=" N ASN A 451 " pdb=" C ASN A 451 " pdb=" CB ASN A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1' DA B 49 " pdb=" O4' DA B 49 " pdb=" C2' DA B 49 " pdb=" N9 DA B 49 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1' C D 83 " pdb=" O4' C D 83 " pdb=" C2' C D 83 " pdb=" N1 C D 83 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1974 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 50 " -0.049 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 C D 50 " 0.043 2.00e-02 2.50e+03 pdb=" C2 C D 50 " -0.011 2.00e-02 2.50e+03 pdb=" O2 C D 50 " 0.010 2.00e-02 2.50e+03 pdb=" N3 C D 50 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C D 50 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C D 50 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C D 50 " -0.038 2.00e-02 2.50e+03 pdb=" C6 C D 50 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 91 " 0.044 2.00e-02 2.50e+03 2.67e-02 1.61e+01 pdb=" N1 C D 91 " -0.049 2.00e-02 2.50e+03 pdb=" C2 C D 91 " -0.000 2.00e-02 2.50e+03 pdb=" O2 C D 91 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C D 91 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C D 91 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C D 91 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C D 91 " 0.030 2.00e-02 2.50e+03 pdb=" C6 C D 91 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 309 " 0.312 9.50e-02 1.11e+02 1.41e-01 1.58e+01 pdb=" NE ARG A 309 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 309 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 309 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 309 " 0.000 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 6227 3.02 - 3.49: 11876 3.49 - 3.96: 21959 3.96 - 4.43: 25254 4.43 - 4.90: 36310 Nonbonded interactions: 101626 Sorted by model distance: nonbonded pdb=" N GLY A 12 " pdb=" O GLY A 12 " model vdw 2.547 2.496 nonbonded pdb=" O ASN A 451 " pdb=" OD1 ASN A 451 " model vdw 2.556 3.040 nonbonded pdb=" N1 G D 22 " pdb=" C4 G D 22 " model vdw 2.577 2.672 nonbonded pdb=" N1 G D 66 " pdb=" C4 G D 66 " model vdw 2.584 2.672 nonbonded pdb=" N1 G D 40 " pdb=" C4 G D 40 " model vdw 2.586 2.672 ... (remaining 101621 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 : 0.005 0.065 12495 Z= 0.328 Angle : 0.979 14.510 17413 Z= 0.661 Chirality : 0.059 0.305 1977 Planarity : 0.009 0.141 1773 Dihedral : 17.982 126.806 5426 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.29 % Allowed : 10.14 % Favored : 89.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1120 helix: -0.15 (0.20), residues: 520 sheet: 0.21 (0.40), residues: 143 loop : 0.36 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG A 309 TYR 0.024 0.004 TYR A1093 PHE 0.042 0.003 PHE A1575 TRP 0.026 0.003 TRP A1458 HIS 0.021 0.002 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.33 (12495) covalent geometry : angle 0.97868 / 0.66 (17413) hydrogen bonds : bond 0.12521 / 13.83 ( 536) hydrogen bonds : angle 5.62876 / 6.88 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8020 (m-10) cc_final: 0.7597 (m-10) REVERT: A 31 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8485 (mmp80) REVERT: A 51 MET cc_start: 0.9358 (mmp) cc_final: 0.8892 (mmp) REVERT: A 299 LYS cc_start: 0.8515 (mmtt) cc_final: 0.7612 (mtmt) REVERT: A 303 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7848 (mm-30) REVERT: A 398 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8418 (mm-30) REVERT: A 478 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 603 GLN cc_start: 0.8954 (pp30) cc_final: 0.8625 (pp30) REVERT: A 621 ARG cc_start: 0.8940 (ttm110) cc_final: 0.8729 (ttp-170) REVERT: A 843 SER cc_start: 0.8557 (t) cc_final: 0.8139 (p) REVERT: A 875 ASP cc_start: 0.8656 (m-30) cc_final: 0.8427 (m-30) REVERT: A 904 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8874 (tp30) REVERT: A 1528 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8736 (ttmm) REVERT: A 1592 ILE cc_start: 0.9434 (mt) cc_final: 0.9233 (mp) REVERT: A 1613 MET cc_start: 0.8844 (mtp) cc_final: 0.8487 (ttt) REVERT: A 1623 ASN cc_start: 0.8354 (m-40) cc_final: 0.7915 (p0) outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 0.6635 time to fit residues: 63.1826 Evaluate side-chains 82 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1215 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.072718 restraints weight = 21288.332| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.16 r_work: 0.2882 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12495 Z= 0.187 Angle : 0.567 6.647 17413 Z= 0.327 Chirality : 0.042 0.236 1977 Planarity : 0.003 0.030 1773 Dihedral : 18.672 134.090 3004 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.25 % Allowed : 9.07 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1120 helix: 1.46 (0.22), residues: 507 sheet: 0.44 (0.36), residues: 151 loop : 0.82 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 619 TYR 0.014 0.002 TYR A1328 PHE 0.017 0.002 PHE A1419 TRP 0.013 0.002 TRP A1458 HIS 0.009 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (12495) covalent geometry : angle 0.56737 / 0.33 (17413) hydrogen bonds : bond 0.04624 / 5.14 ( 536) hydrogen bonds : angle 4.26659 / 5.15 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8923 (tpp80) cc_final: 0.8444 (mmp80) REVERT: A 299 LYS cc_start: 0.8476 (mmtt) cc_final: 0.7555 (mtmt) REVERT: A 303 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7945 (mm-30) REVERT: A 398 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8353 (mm-30) REVERT: A 451 ASN cc_start: 0.8995 (p0) cc_final: 0.8748 (p0) REVERT: A 478 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 577 LYS cc_start: 0.8902 (pmtt) cc_final: 0.8608 (pmtt) REVERT: A 603 GLN cc_start: 0.9044 (pp30) cc_final: 0.8668 (pp30) REVERT: A 621 ARG cc_start: 0.8975 (ttm110) cc_final: 0.8743 (ttp-170) REVERT: A 843 SER cc_start: 0.8401 (t) cc_final: 0.7853 (p) REVERT: A 875 ASP cc_start: 0.8775 (m-30) cc_final: 0.8516 (m-30) REVERT: A 889 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 1528 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8840 (ttmm) REVERT: A 1591 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 1592 ILE cc_start: 0.9452 (mt) cc_final: 0.9178 (mp) REVERT: A 1623 ASN cc_start: 0.8256 (m-40) cc_final: 0.7886 (p0) outliers start: 13 outliers final: 4 residues processed: 89 average time/residue: 0.6543 time to fit residues: 63.0345 Evaluate side-chains 81 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1590 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071163 restraints weight = 21203.858| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.18 r_work: 0.2881 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12495 Z= 0.160 Angle : 0.524 6.656 17413 Z= 0.303 Chirality : 0.040 0.218 1977 Planarity : 0.003 0.031 1773 Dihedral : 18.668 137.859 3002 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.35 % Allowed : 8.98 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1120 helix: 1.92 (0.22), residues: 505 sheet: 0.46 (0.37), residues: 150 loop : 0.95 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 619 TYR 0.013 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.010 0.001 TRP A1458 HIS 0.009 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (12495) covalent geometry : angle 0.52377 / 0.30 (17413) hydrogen bonds : bond 0.04111 / 4.54 ( 536) hydrogen bonds : angle 3.90832 / 4.63 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8094 (m-10) cc_final: 0.7870 (m-10) REVERT: A 31 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8505 (mmp80) REVERT: A 41 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: A 299 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7586 (mtmt) REVERT: A 398 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8305 (mm-30) REVERT: A 451 ASN cc_start: 0.9032 (p0) cc_final: 0.8681 (p0) REVERT: A 478 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8288 (tm-30) REVERT: A 603 GLN cc_start: 0.9028 (pp30) cc_final: 0.8654 (pp30) REVERT: A 621 ARG cc_start: 0.8991 (ttm110) cc_final: 0.8762 (ttp-170) REVERT: A 843 SER cc_start: 0.8380 (t) cc_final: 0.7859 (p) REVERT: A 875 ASP cc_start: 0.8773 (m-30) cc_final: 0.8502 (m-30) REVERT: A 889 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8019 (mm-40) REVERT: A 1303 ILE cc_start: 0.8994 (pt) cc_final: 0.8783 (pp) REVERT: A 1528 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8900 (ttmm) REVERT: A 1591 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 1592 ILE cc_start: 0.9441 (mt) cc_final: 0.9190 (mp) REVERT: A 1623 ASN cc_start: 0.8223 (m-40) cc_final: 0.7911 (p0) outliers start: 14 outliers final: 6 residues processed: 90 average time/residue: 0.6123 time to fit residues: 59.5105 Evaluate side-chains 81 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 84 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.0000 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.099658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073238 restraints weight = 21225.596| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.16 r_work: 0.2898 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12495 Z= 0.124 Angle : 0.490 7.435 17413 Z= 0.285 Chirality : 0.039 0.211 1977 Planarity : 0.003 0.029 1773 Dihedral : 18.689 139.883 3002 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.16 % Allowed : 9.94 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.25), residues: 1120 helix: 2.11 (0.23), residues: 505 sheet: 0.48 (0.37), residues: 150 loop : 0.95 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 619 TYR 0.012 0.001 TYR A1328 PHE 0.016 0.001 PHE A1419 TRP 0.010 0.001 TRP A 78 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12495) covalent geometry : angle 0.49019 / 0.28 (17413) hydrogen bonds : bond 0.03789 / 4.16 ( 536) hydrogen bonds : angle 3.75722 / 4.44 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8918 (tpp80) cc_final: 0.8547 (mmp80) REVERT: A 299 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7570 (mtmt) REVERT: A 398 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8311 (mm-30) REVERT: A 451 ASN cc_start: 0.9016 (p0) cc_final: 0.8647 (p0) REVERT: A 478 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 603 GLN cc_start: 0.9050 (pp30) cc_final: 0.8658 (pp30) REVERT: A 843 SER cc_start: 0.8362 (t) cc_final: 0.7850 (p) REVERT: A 875 ASP cc_start: 0.8774 (m-30) cc_final: 0.8498 (m-30) REVERT: A 889 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8068 (mm-40) REVERT: A 1303 ILE cc_start: 0.8999 (pt) cc_final: 0.8796 (pp) REVERT: A 1528 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8922 (ttmm) REVERT: A 1591 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 1592 ILE cc_start: 0.9422 (mt) cc_final: 0.9215 (mp) REVERT: A 1623 ASN cc_start: 0.8214 (m-40) cc_final: 0.7905 (p0) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.6312 time to fit residues: 58.9946 Evaluate side-chains 75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1590 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 68 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 666 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072584 restraints weight = 21189.430| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.15 r_work: 0.2881 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12495 Z= 0.142 Angle : 0.485 7.443 17413 Z= 0.281 Chirality : 0.039 0.211 1977 Planarity : 0.003 0.031 1773 Dihedral : 18.681 141.368 3002 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.16 % Allowed : 10.14 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.25), residues: 1120 helix: 2.18 (0.23), residues: 506 sheet: 0.46 (0.38), residues: 150 loop : 0.89 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1559 TYR 0.013 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.010 0.001 TRP A 78 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12495) covalent geometry : angle 0.48471 / 0.28 (17413) hydrogen bonds : bond 0.03747 / 4.12 ( 536) hydrogen bonds : angle 3.68656 / 4.33 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8306 (m-10) cc_final: 0.7143 (m-80) REVERT: A 31 ARG cc_start: 0.8931 (tpp80) cc_final: 0.8585 (mmp80) REVERT: A 299 LYS cc_start: 0.8503 (mmtt) cc_final: 0.7634 (mtmt) REVERT: A 398 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8290 (mm-30) REVERT: A 451 ASN cc_start: 0.9005 (p0) cc_final: 0.8610 (p0) REVERT: A 478 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 603 GLN cc_start: 0.9012 (pp30) cc_final: 0.8645 (pp30) REVERT: A 843 SER cc_start: 0.8381 (t) cc_final: 0.7892 (p) REVERT: A 852 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 875 ASP cc_start: 0.8758 (m-30) cc_final: 0.8486 (m-30) REVERT: A 889 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7464 (tm-30) REVERT: A 1303 ILE cc_start: 0.9005 (pt) cc_final: 0.8794 (pp) REVERT: A 1528 LYS cc_start: 0.9268 (ttmm) cc_final: 0.8938 (ttmm) REVERT: A 1591 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 1613 MET cc_start: 0.8843 (ttp) cc_final: 0.8566 (ttt) REVERT: A 1623 ASN cc_start: 0.8222 (m-40) cc_final: 0.7915 (p0) outliers start: 12 outliers final: 4 residues processed: 83 average time/residue: 0.6061 time to fit residues: 54.6457 Evaluate side-chains 77 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.070975 restraints weight = 21186.118| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.17 r_work: 0.2878 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12495 Z= 0.151 Angle : 0.492 8.085 17413 Z= 0.283 Chirality : 0.039 0.212 1977 Planarity : 0.003 0.030 1773 Dihedral : 18.691 142.024 3002 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.45 % Allowed : 9.94 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.25), residues: 1120 helix: 2.18 (0.23), residues: 507 sheet: 0.37 (0.37), residues: 157 loop : 0.91 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 619 TYR 0.013 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.010 0.001 TRP A 78 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (12495) covalent geometry : angle 0.49230 / 0.28 (17413) hydrogen bonds : bond 0.03720 / 4.08 ( 536) hydrogen bonds : angle 3.69974 / 4.35 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8264 (m-10) cc_final: 0.8042 (m-80) REVERT: A 31 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8615 (mmp80) REVERT: A 41 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: A 299 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7688 (mtmt) REVERT: A 398 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8280 (mm-30) REVERT: A 451 ASN cc_start: 0.8992 (p0) cc_final: 0.8603 (p0) REVERT: A 478 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 603 GLN cc_start: 0.9015 (pp30) cc_final: 0.8634 (pp30) REVERT: A 664 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8386 (ptm-80) REVERT: A 843 SER cc_start: 0.8387 (t) cc_final: 0.7919 (p) REVERT: A 852 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 875 ASP cc_start: 0.8765 (m-30) cc_final: 0.8484 (m-30) REVERT: A 889 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8052 (mm-40) REVERT: A 1185 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 1303 ILE cc_start: 0.9008 (pt) cc_final: 0.8803 (pp) REVERT: A 1528 LYS cc_start: 0.9276 (ttmm) cc_final: 0.8942 (ttmm) REVERT: A 1591 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 1613 MET cc_start: 0.8907 (ttp) cc_final: 0.8559 (ttt) REVERT: A 1623 ASN cc_start: 0.8261 (m-40) cc_final: 0.7972 (p0) outliers start: 15 outliers final: 4 residues processed: 85 average time/residue: 0.5591 time to fit residues: 51.4253 Evaluate side-chains 79 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1566 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071923 restraints weight = 21148.090| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.15 r_work: 0.2897 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12495 Z= 0.123 Angle : 0.489 10.130 17413 Z= 0.279 Chirality : 0.038 0.205 1977 Planarity : 0.003 0.029 1773 Dihedral : 18.696 143.290 3002 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.16 % Allowed : 10.52 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.25), residues: 1120 helix: 2.23 (0.23), residues: 506 sheet: 0.47 (0.38), residues: 152 loop : 0.93 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 619 TYR 0.012 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.011 0.001 TRP A 78 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12495) covalent geometry : angle 0.48850 / 0.28 (17413) hydrogen bonds : bond 0.03550 / 3.88 ( 536) hydrogen bonds : angle 3.65078 / 4.25 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8300 (m-10) cc_final: 0.8099 (m-80) REVERT: A 31 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8654 (mmp80) REVERT: A 41 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: A 299 LYS cc_start: 0.8542 (mmtt) cc_final: 0.7671 (mtmt) REVERT: A 451 ASN cc_start: 0.8934 (p0) cc_final: 0.8566 (p0) REVERT: A 478 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 603 GLN cc_start: 0.9007 (pp30) cc_final: 0.8622 (pp30) REVERT: A 843 SER cc_start: 0.8367 (t) cc_final: 0.7898 (p) REVERT: A 852 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 875 ASP cc_start: 0.8703 (m-30) cc_final: 0.8431 (m-30) REVERT: A 889 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 1185 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 1303 ILE cc_start: 0.8989 (pt) cc_final: 0.8780 (pp) REVERT: A 1528 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8939 (ttmm) REVERT: A 1613 MET cc_start: 0.8909 (ttp) cc_final: 0.8587 (ttt) REVERT: A 1623 ASN cc_start: 0.8294 (m-40) cc_final: 0.8009 (p0) outliers start: 12 outliers final: 5 residues processed: 87 average time/residue: 0.5654 time to fit residues: 53.4266 Evaluate side-chains 82 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1566 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 69 optimal weight: 0.0170 chunk 64 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071874 restraints weight = 21100.598| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.15 r_work: 0.2899 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12495 Z= 0.128 Angle : 0.476 7.255 17413 Z= 0.275 Chirality : 0.038 0.204 1977 Planarity : 0.003 0.030 1773 Dihedral : 18.686 143.684 3002 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.06 % Allowed : 11.78 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.25), residues: 1120 helix: 2.29 (0.23), residues: 506 sheet: 0.39 (0.37), residues: 157 loop : 0.90 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.012 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.010 0.001 TRP A 78 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (12495) covalent geometry : angle 0.47551 / 0.27 (17413) hydrogen bonds : bond 0.03531 / 3.86 ( 536) hydrogen bonds : angle 3.62142 / 4.24 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8981 (tpp80) cc_final: 0.8662 (mmp80) REVERT: A 41 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: A 299 LYS cc_start: 0.8564 (mmtt) cc_final: 0.7683 (mtmt) REVERT: A 451 ASN cc_start: 0.8932 (p0) cc_final: 0.8565 (p0) REVERT: A 478 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 603 GLN cc_start: 0.9016 (pp30) cc_final: 0.8625 (pp30) REVERT: A 843 SER cc_start: 0.8337 (t) cc_final: 0.7856 (p) REVERT: A 875 ASP cc_start: 0.8714 (m-30) cc_final: 0.8442 (m-30) REVERT: A 889 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8046 (mm-40) REVERT: A 1185 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 1303 ILE cc_start: 0.8961 (pt) cc_final: 0.8758 (pp) REVERT: A 1528 LYS cc_start: 0.9283 (ttmm) cc_final: 0.8946 (ttmm) REVERT: A 1613 MET cc_start: 0.8924 (ttp) cc_final: 0.8583 (ttt) REVERT: A 1623 ASN cc_start: 0.8297 (m-40) cc_final: 0.8008 (p0) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.6057 time to fit residues: 54.7173 Evaluate side-chains 83 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1566 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.0570 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070246 restraints weight = 21006.805| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.15 r_work: 0.2869 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12495 Z= 0.174 Angle : 0.522 9.687 17413 Z= 0.294 Chirality : 0.039 0.214 1977 Planarity : 0.003 0.032 1773 Dihedral : 18.684 142.889 3002 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.87 % Allowed : 11.68 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1120 helix: 2.20 (0.23), residues: 510 sheet: 0.39 (0.38), residues: 157 loop : 0.80 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.013 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.009 0.001 TRP A 78 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (12495) covalent geometry : angle 0.52163 / 0.29 (17413) hydrogen bonds : bond 0.03722 / 4.08 ( 536) hydrogen bonds : angle 3.69774 / 4.33 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8966 (tpp80) cc_final: 0.8653 (mmp80) REVERT: A 41 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: A 299 LYS cc_start: 0.8604 (mmtt) cc_final: 0.7726 (mtmt) REVERT: A 451 ASN cc_start: 0.8999 (p0) cc_final: 0.8618 (p0) REVERT: A 478 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 603 GLN cc_start: 0.9000 (pp30) cc_final: 0.8589 (pp30) REVERT: A 843 SER cc_start: 0.8391 (t) cc_final: 0.7922 (p) REVERT: A 847 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: A 875 ASP cc_start: 0.8751 (m-30) cc_final: 0.8458 (m-30) REVERT: A 889 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8094 (mm-40) REVERT: A 1185 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8330 (mm-30) REVERT: A 1303 ILE cc_start: 0.8972 (pt) cc_final: 0.8760 (pp) REVERT: A 1528 LYS cc_start: 0.9293 (ttmm) cc_final: 0.8959 (ttmm) REVERT: A 1613 MET cc_start: 0.8915 (ttp) cc_final: 0.8593 (ttt) REVERT: A 1623 ASN cc_start: 0.8321 (m-40) cc_final: 0.8054 (p0) outliers start: 9 outliers final: 5 residues processed: 81 average time/residue: 0.5824 time to fit residues: 51.4114 Evaluate side-chains 80 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1566 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071213 restraints weight = 21112.799| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.16 r_work: 0.2890 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 : 0.003 0.053 12495 Z= 0.132 Angle : 0.491 7.792 17413 Z= 0.282 Chirality : 0.038 0.210 1977 Planarity : 0.003 0.032 1773 Dihedral : 18.699 143.601 3002 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.97 % Allowed : 11.58 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1120 helix: 2.20 (0.23), residues: 511 sheet: 0.38 (0.38), residues: 157 loop : 0.85 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.012 0.001 TYR A1328 PHE 0.016 0.001 PHE A 2 TRP 0.010 0.001 TRP A 78 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12495) covalent geometry : angle 0.49088 / 0.28 (17413) hydrogen bonds : bond 0.03548 / 3.87 ( 536) hydrogen bonds : angle 3.65180 / 4.29 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8650 (mmp80) REVERT: A 41 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: A 299 LYS cc_start: 0.8588 (mmtt) cc_final: 0.7679 (mtmt) REVERT: A 451 ASN cc_start: 0.8962 (p0) cc_final: 0.8562 (p0) REVERT: A 478 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 603 GLN cc_start: 0.9017 (pp30) cc_final: 0.8598 (pp30) REVERT: A 843 SER cc_start: 0.8375 (t) cc_final: 0.7899 (p) REVERT: A 847 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: A 875 ASP cc_start: 0.8734 (m-30) cc_final: 0.8444 (m-30) REVERT: A 889 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8103 (mm-40) REVERT: A 1185 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 1528 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8942 (ttmm) REVERT: A 1613 MET cc_start: 0.8935 (ttp) cc_final: 0.8633 (ttt) REVERT: A 1623 ASN cc_start: 0.8329 (m-40) cc_final: 0.8055 (p0) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.5921 time to fit residues: 50.8993 Evaluate side-chains 79 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1566 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071190 restraints weight = 21080.346| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.15 r_work: 0.2889 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 : 0.003 0.053 12495 Z= 0.135 Angle : 0.502 9.805 17413 Z= 0.285 Chirality : 0.039 0.209 1977 Planarity : 0.003 0.032 1773 Dihedral : 18.674 144.029 3002 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.68 % Allowed : 12.16 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1120 helix: 2.24 (0.23), residues: 511 sheet: 0.40 (0.38), residues: 157 loop : 0.84 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.012 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.010 0.001 TRP A 78 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12495) covalent geometry : angle 0.50157 / 0.28 (17413) hydrogen bonds : bond 0.03537 / 3.86 ( 536) hydrogen bonds : angle 3.64623 / 4.26 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.62 seconds wall clock time: 60 minutes 42.48 seconds (3642.48 seconds total)