Starting phenix.real_space_refine on Wed Feb 4 18:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6t_49074/02_2026/9n6t_49074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6t_49074/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9n6t_49074/02_2026/9n6t_49074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6t_49074/02_2026/9n6t_49074.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n6t_49074/02_2026/9n6t_49074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6t_49074/02_2026/9n6t_49074.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 2.45, 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: 0.89 Conformation dependent library (CDL) restraints added in 486.8 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: 1.55 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: 2.77 Time building geometry restraints manager: 1.20 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=" CG LYS A 378 " pdb=" CD LYS A 378 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.73e+00 bond pdb=" C LEU A1507 " pdb=" N PRO A1508 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.51e-02 4.39e+03 4.70e+00 bond pdb=" CA ILE A 926 " pdb=" CB ILE A 926 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.30e-02 5.92e+03 4.02e+00 bond pdb=" CB LYS A 378 " pdb=" CG LYS A 378 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.78e+00 bond pdb=" CB ASN A1128 " pdb=" CG ASN A1128 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.36e+00 ... (remaining 12490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 17088 2.90 - 5.80: 276 5.80 - 8.71: 40 8.71 - 11.61: 4 11.61 - 14.51: 5 Bond angle restraints: 17413 Sorted by residual: angle pdb=" CB LYS A 378 " pdb=" CG LYS A 378 " pdb=" CD LYS A 378 " ideal model delta sigma weight residual 111.30 125.42 -14.12 2.30e+00 1.89e-01 3.77e+01 angle pdb=" CA GLN A1595 " pdb=" CB GLN A1595 " pdb=" CG GLN A1595 " ideal model delta sigma weight residual 114.10 125.67 -11.57 2.00e+00 2.50e-01 3.35e+01 angle pdb=" O3' U D 21 " pdb=" P G D 22 " pdb=" O5' G D 22 " ideal model delta sigma weight residual 104.00 111.55 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" CG1 ILE A 926 " pdb=" CB ILE A 926 " pdb=" CG2 ILE A 926 " ideal model delta sigma weight residual 110.70 96.19 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CB LYS A1561 " pdb=" CG LYS A1561 " pdb=" CD LYS A1561 " ideal model delta sigma weight residual 111.30 122.34 -11.04 2.30e+00 1.89e-01 2.31e+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: 1518 0.061 - 0.122: 365 0.122 - 0.183: 71 0.183 - 0.244: 20 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 2.42 2.13 0.29 2.00e-01 2.50e+01 2.08e+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: 7.440 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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= 0.231 Angle : 0.963 14.510 17413 Z= 0.541 Chirality : 0.058 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 covalent geometry : bond 0.00488 (12495) covalent geometry : angle 0.96315 (17413) hydrogen bonds : bond 0.12521 ( 536) hydrogen bonds : angle 5.62876 ( 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 : 0.389 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: 0.5890 time to fit residues: 55.8684 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 : 0.384 ------------------------------------------------------------------------------- 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: 2.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071971 restraints weight = 21278.014| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.19 r_work: 0.2880 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12495 Z= 0.194 Angle : 0.580 7.692 17413 Z= 0.314 Chirality : 0.040 0.221 1977 Planarity : 0.003 0.032 1773 Dihedral : 18.662 128.297 3004 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.45 % Allowed : 9.17 % Favored : 89.38 % 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: 1.56 (0.24), residues: 1120 helix: 1.51 (0.22), residues: 506 sheet: 0.45 (0.37), residues: 150 loop : 0.92 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 619 TYR 0.013 0.001 TYR A1328 PHE 0.017 0.002 PHE A1232 TRP 0.012 0.002 TRP A1458 HIS 0.009 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00432 (12495) covalent geometry : angle 0.57972 (17413) hydrogen bonds : bond 0.04062 ( 536) hydrogen bonds : angle 4.12250 ( 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 102 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8454 (mmp80) REVERT: A 41 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: A 299 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7579 (mtmt) REVERT: A 303 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7939 (mm-30) REVERT: A 398 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8366 (mm-30) REVERT: A 451 ASN cc_start: 0.9020 (p0) cc_final: 0.8764 (p0) REVERT: A 478 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8280 (tm-30) REVERT: A 603 GLN cc_start: 0.9050 (pp30) cc_final: 0.8670 (pp30) REVERT: A 621 ARG cc_start: 0.8981 (ttm110) cc_final: 0.8742 (ttp-170) REVERT: A 843 SER cc_start: 0.8396 (t) cc_final: 0.7901 (p) REVERT: A 875 ASP cc_start: 0.8778 (m-30) cc_final: 0.8482 (m-30) REVERT: A 889 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8321 (mm-40) REVERT: A 1303 ILE cc_start: 0.8985 (pt) cc_final: 0.8775 (pp) REVERT: A 1528 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8852 (ttmm) REVERT: A 1591 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 1592 ILE cc_start: 0.9454 (mt) cc_final: 0.9195 (mp) REVERT: A 1623 ASN cc_start: 0.8243 (m-40) cc_final: 0.7939 (p0) outliers start: 15 outliers final: 4 residues processed: 93 average time/residue: 0.6438 time to fit residues: 64.5871 Evaluate side-chains 83 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 666 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068749 restraints weight = 21276.435| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.17 r_work: 0.2836 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12495 Z= 0.225 Angle : 0.572 7.278 17413 Z= 0.309 Chirality : 0.041 0.227 1977 Planarity : 0.003 0.034 1773 Dihedral : 18.627 128.635 3002 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.35 % Allowed : 9.27 % Favored : 89.38 % 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: 1.79 (0.25), residues: 1120 helix: 1.85 (0.22), residues: 504 sheet: 0.40 (0.37), residues: 156 loop : 0.91 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 619 TYR 0.014 0.002 TYR A1328 PHE 0.017 0.002 PHE A1419 TRP 0.011 0.002 TRP A 476 HIS 0.008 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00505 (12495) covalent geometry : angle 0.57170 (17413) hydrogen bonds : bond 0.04038 ( 536) hydrogen bonds : angle 3.91858 ( 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 101 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8572 (mmp80) REVERT: A 299 LYS cc_start: 0.8537 (mmtt) cc_final: 0.7643 (mtmt) REVERT: A 398 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8321 (mm-30) REVERT: A 451 ASN cc_start: 0.9096 (p0) cc_final: 0.8735 (p0) REVERT: A 478 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 577 LYS cc_start: 0.8917 (pmtt) cc_final: 0.8647 (pmtt) REVERT: A 603 GLN cc_start: 0.9038 (pp30) cc_final: 0.8616 (pp30) REVERT: A 843 SER cc_start: 0.8420 (t) cc_final: 0.7927 (p) REVERT: A 852 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 875 ASP cc_start: 0.8816 (m-30) cc_final: 0.8524 (m-30) REVERT: A 889 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8241 (mm-40) REVERT: A 1185 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8332 (mm-30) REVERT: A 1528 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8912 (ttmm) REVERT: A 1568 ASP cc_start: 0.8185 (t0) cc_final: 0.7755 (t0) REVERT: A 1591 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 1592 ILE cc_start: 0.9455 (mt) cc_final: 0.9250 (mp) REVERT: A 1623 ASN cc_start: 0.8264 (m-40) cc_final: 0.7989 (p0) outliers start: 14 outliers final: 6 residues processed: 94 average time/residue: 0.6245 time to fit residues: 63.1515 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 : 0.432 ------------------------------------------------------------------------------- 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 852 ILE Chi-restraints excluded: chain A residue 1211 ILE 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: 0.9980 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070284 restraints weight = 21230.350| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.15 r_work: 0.2867 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12495 Z= 0.146 Angle : 0.514 7.283 17413 Z= 0.280 Chirality : 0.038 0.214 1977 Planarity : 0.003 0.032 1773 Dihedral : 18.635 128.903 3002 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.64 % Allowed : 9.75 % 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: 1.93 (0.25), residues: 1120 helix: 2.07 (0.23), residues: 506 sheet: 0.41 (0.38), residues: 156 loop : 0.85 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 619 TYR 0.013 0.001 TYR A1328 PHE 0.016 0.001 PHE A1419 TRP 0.011 0.001 TRP A 78 HIS 0.007 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00319 (12495) covalent geometry : angle 0.51446 (17413) hydrogen bonds : bond 0.03537 ( 536) hydrogen bonds : angle 3.73764 ( 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 95 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8609 (mmp80) REVERT: A 41 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: A 299 LYS cc_start: 0.8536 (mmtt) cc_final: 0.7677 (mtmt) REVERT: A 398 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8321 (mm-30) REVERT: A 451 ASN cc_start: 0.9029 (p0) cc_final: 0.8654 (p0) REVERT: A 478 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 603 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8624 (pp30) REVERT: A 843 SER cc_start: 0.8386 (t) cc_final: 0.7905 (p) REVERT: A 852 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8610 (mp) REVERT: A 875 ASP cc_start: 0.8812 (m-30) cc_final: 0.8516 (m-30) REVERT: A 889 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8041 (mm-40) REVERT: A 1185 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8361 (mm-30) REVERT: A 1303 ILE cc_start: 0.8951 (pt) cc_final: 0.8731 (pp) REVERT: A 1528 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8899 (ttmm) REVERT: A 1591 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8656 (tm-30) REVERT: A 1613 MET cc_start: 0.8928 (mtp) cc_final: 0.8513 (ttt) REVERT: A 1623 ASN cc_start: 0.8261 (m-40) cc_final: 0.7998 (p0) outliers start: 17 outliers final: 5 residues processed: 88 average time/residue: 0.6188 time to fit residues: 58.9668 Evaluate side-chains 80 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1211 ILE 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: 3.9990 chunk 104 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 0.0010 chunk 103 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070691 restraints weight = 21216.755| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.16 r_work: 0.2897 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12495 Z= 0.135 Angle : 0.503 7.406 17413 Z= 0.273 Chirality : 0.037 0.209 1977 Planarity : 0.003 0.031 1773 Dihedral : 18.619 128.934 3002 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.06 % Allowed : 10.33 % 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: 2.02 (0.25), residues: 1120 helix: 2.18 (0.23), residues: 507 sheet: 0.41 (0.38), residues: 156 loop : 0.88 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 619 TYR 0.013 0.001 TYR A1328 PHE 0.016 0.001 PHE A1419 TRP 0.011 0.001 TRP A 78 HIS 0.006 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00299 (12495) covalent geometry : angle 0.50304 (17413) hydrogen bonds : bond 0.03383 ( 536) hydrogen bonds : angle 3.67575 ( 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 89 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8330 (m-80) cc_final: 0.8054 (m-80) REVERT: A 31 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8631 (mmp80) REVERT: A 41 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: A 299 LYS cc_start: 0.8594 (mmtt) cc_final: 0.7721 (mtmt) REVERT: A 451 ASN cc_start: 0.9003 (p0) cc_final: 0.8617 (p0) REVERT: A 478 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 603 GLN cc_start: 0.9042 (pp30) cc_final: 0.8624 (pp30) REVERT: A 664 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8452 (ptm-80) REVERT: A 843 SER cc_start: 0.8387 (t) cc_final: 0.7921 (p) REVERT: A 852 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 875 ASP cc_start: 0.8784 (m-30) cc_final: 0.8487 (m-30) REVERT: A 889 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7898 (mm-40) REVERT: A 1185 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 1303 ILE cc_start: 0.8936 (pt) cc_final: 0.8717 (pp) REVERT: A 1528 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8940 (ttmm) REVERT: A 1623 ASN cc_start: 0.8257 (m-40) cc_final: 0.8002 (p0) outliers start: 11 outliers final: 3 residues processed: 85 average time/residue: 0.6769 time to fit residues: 62.0279 Evaluate side-chains 80 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 350 LYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069671 restraints weight = 21220.053| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.16 r_work: 0.2858 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12495 Z= 0.172 Angle : 0.519 9.040 17413 Z= 0.279 Chirality : 0.039 0.214 1977 Planarity : 0.003 0.030 1773 Dihedral : 18.613 129.117 3002 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.35 % Allowed : 11.29 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.25), residues: 1120 helix: 2.18 (0.23), residues: 509 sheet: 0.35 (0.37), residues: 157 loop : 0.78 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.014 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 covalent geometry : bond 0.00383 (12495) covalent geometry : angle 0.51910 (17413) hydrogen bonds : bond 0.03490 ( 536) hydrogen bonds : angle 3.64212 ( 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 89 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8402 (m-80) cc_final: 0.7784 (m-10) REVERT: A 31 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8679 (mmp80) REVERT: A 41 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: A 299 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7682 (mtmt) REVERT: A 451 ASN cc_start: 0.9035 (p0) cc_final: 0.8632 (p0) REVERT: A 478 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 603 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8629 (pp30) REVERT: A 664 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8509 (ptm-80) REVERT: A 843 SER cc_start: 0.8404 (t) cc_final: 0.7938 (p) REVERT: A 847 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 875 ASP cc_start: 0.8799 (m-30) cc_final: 0.8506 (m-30) REVERT: A 889 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7719 (mm-40) REVERT: A 1185 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 1303 ILE cc_start: 0.8920 (pt) cc_final: 0.8700 (pp) REVERT: A 1528 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8933 (ttmm) REVERT: A 1613 MET cc_start: 0.8962 (mtp) cc_final: 0.8486 (ttt) REVERT: A 1623 ASN cc_start: 0.8273 (m-40) cc_final: 0.8007 (p0) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 0.6245 time to fit residues: 56.5369 Evaluate side-chains 84 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 664 ARG 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 Chi-restraints excluded: chain A residue 1616 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068831 restraints weight = 21241.116| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.15 r_work: 0.2834 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12495 Z= 0.197 Angle : 0.532 7.935 17413 Z= 0.286 Chirality : 0.039 0.222 1977 Planarity : 0.003 0.030 1773 Dihedral : 18.640 129.559 3002 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.35 % Allowed : 11.49 % 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: 1.94 (0.25), residues: 1120 helix: 2.18 (0.23), residues: 507 sheet: 0.35 (0.37), residues: 157 loop : 0.76 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 619 TYR 0.014 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 A 59 Details of bonding type rmsd covalent geometry : bond 0.00441 (12495) covalent geometry : angle 0.53224 (17413) hydrogen bonds : bond 0.03585 ( 536) hydrogen bonds : angle 3.70730 ( 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 88 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8417 (m-80) cc_final: 0.8093 (m-80) REVERT: A 31 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8669 (mmp80) REVERT: A 41 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: A 299 LYS cc_start: 0.8591 (mmtt) cc_final: 0.7713 (mtmt) REVERT: A 451 ASN cc_start: 0.9067 (p0) cc_final: 0.8646 (p0) REVERT: A 478 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 603 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8610 (pp30) REVERT: A 664 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8544 (ptm160) REVERT: A 843 SER cc_start: 0.8453 (t) cc_final: 0.7999 (p) REVERT: A 875 ASP cc_start: 0.8784 (m-30) cc_final: 0.8498 (m-30) REVERT: A 889 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8018 (mm-40) REVERT: A 1185 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8468 (mm-30) REVERT: A 1303 ILE cc_start: 0.8910 (pt) cc_final: 0.8686 (pp) REVERT: A 1528 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8926 (ttmm) REVERT: A 1613 MET cc_start: 0.8934 (mtp) cc_final: 0.8537 (ttt) REVERT: A 1623 ASN cc_start: 0.8285 (m-40) cc_final: 0.8052 (p0) outliers start: 14 outliers final: 4 residues processed: 82 average time/residue: 0.5885 time to fit residues: 52.1706 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 664 ARG 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: 0.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069618 restraints weight = 21187.645| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.14 r_work: 0.2855 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12495 Z= 0.161 Angle : 0.515 9.039 17413 Z= 0.278 Chirality : 0.038 0.218 1977 Planarity : 0.003 0.030 1773 Dihedral : 18.644 129.749 3002 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.35 % Allowed : 11.87 % Favored : 86.78 % 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: 1.94 (0.25), residues: 1120 helix: 2.18 (0.23), residues: 510 sheet: 0.33 (0.37), residues: 157 loop : 0.74 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.014 0.001 TYR A1328 PHE 0.016 0.001 PHE A1419 TRP 0.011 0.001 TRP A 78 HIS 0.005 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00360 (12495) covalent geometry : angle 0.51530 (17413) hydrogen bonds : bond 0.03417 ( 536) hydrogen bonds : angle 3.66829 ( 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 91 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8448 (m-80) cc_final: 0.8114 (m-80) REVERT: A 31 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8687 (mmp80) REVERT: A 41 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: A 299 LYS cc_start: 0.8611 (mmtt) cc_final: 0.7776 (mtmt) REVERT: A 451 ASN cc_start: 0.9048 (p0) cc_final: 0.8649 (p0) REVERT: A 478 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 603 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8611 (pp30) REVERT: A 664 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8583 (ptm160) REVERT: A 843 SER cc_start: 0.8416 (t) cc_final: 0.7958 (p) REVERT: A 847 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8481 (mt0) REVERT: A 852 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8833 (mp) REVERT: A 875 ASP cc_start: 0.8775 (m-30) cc_final: 0.8479 (m-30) REVERT: A 889 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8011 (mm-40) REVERT: A 1185 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 1303 ILE cc_start: 0.8919 (pt) cc_final: 0.8698 (pp) REVERT: A 1528 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8945 (ttmm) REVERT: A 1613 MET cc_start: 0.8927 (mtp) cc_final: 0.8537 (ttt) REVERT: A 1623 ASN cc_start: 0.8265 (m-40) cc_final: 0.8031 (p0) outliers start: 14 outliers final: 4 residues processed: 84 average time/residue: 0.6178 time to fit residues: 56.0500 Evaluate side-chains 80 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 664 ARG 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=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: 0.6980 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069562 restraints weight = 21076.592| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.13 r_work: 0.2856 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12495 Z= 0.170 Angle : 0.520 8.319 17413 Z= 0.281 Chirality : 0.038 0.221 1977 Planarity : 0.003 0.034 1773 Dihedral : 18.636 130.020 3002 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.45 % Allowed : 11.87 % Favored : 86.68 % 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: 1.96 (0.25), residues: 1120 helix: 2.20 (0.23), residues: 508 sheet: 0.29 (0.38), residues: 157 loop : 0.79 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 632 TYR 0.014 0.001 TYR A1328 PHE 0.016 0.001 PHE A1419 TRP 0.010 0.001 TRP A 78 HIS 0.005 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00380 (12495) covalent geometry : angle 0.51974 (17413) hydrogen bonds : bond 0.03441 ( 536) hydrogen bonds : angle 3.69032 ( 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 90 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8428 (m-80) cc_final: 0.8118 (m-80) REVERT: A 31 ARG cc_start: 0.8989 (tpp80) cc_final: 0.8715 (mmp80) REVERT: A 41 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: A 299 LYS cc_start: 0.8611 (mmtt) cc_final: 0.7774 (mtmt) REVERT: A 451 ASN cc_start: 0.9045 (p0) cc_final: 0.8634 (p0) REVERT: A 478 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 603 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8608 (pp30) REVERT: A 664 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8609 (ptm160) REVERT: A 843 SER cc_start: 0.8428 (t) cc_final: 0.7969 (p) REVERT: A 847 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: A 852 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 875 ASP cc_start: 0.8777 (m-30) cc_final: 0.8474 (m-30) REVERT: A 889 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 1185 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 1303 ILE cc_start: 0.8915 (pt) cc_final: 0.8693 (pp) REVERT: A 1528 LYS cc_start: 0.9252 (ttmm) cc_final: 0.8953 (ttmm) REVERT: A 1623 ASN cc_start: 0.8266 (m-40) cc_final: 0.8036 (p0) outliers start: 15 outliers final: 5 residues processed: 84 average time/residue: 0.6226 time to fit residues: 56.3825 Evaluate side-chains 82 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 664 ARG 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 1427 LYS 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: 0.6980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.067130 restraints weight = 21186.137| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.22 r_work: 0.2754 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12495 Z= 0.153 Angle : 0.531 10.237 17413 Z= 0.284 Chirality : 0.038 0.219 1977 Planarity : 0.003 0.032 1773 Dihedral : 18.638 130.198 3002 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.06 % Allowed : 12.26 % Favored : 86.68 % 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: 1.94 (0.25), residues: 1120 helix: 2.19 (0.23), residues: 511 sheet: 0.28 (0.38), residues: 157 loop : 0.76 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 632 TYR 0.014 0.001 TYR A1328 PHE 0.016 0.001 PHE A1419 TRP 0.011 0.001 TRP A 78 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00345 (12495) covalent geometry : angle 0.53092 (17413) hydrogen bonds : bond 0.03356 ( 536) hydrogen bonds : angle 3.66707 ( 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: 11 poor density : 72 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 2 PHE cc_start: 0.8394 (m-80) cc_final: 0.8033 (m-80) REVERT: A 31 ARG cc_start: 0.8982 (tpp80) cc_final: 0.8698 (mmp80) REVERT: A 41 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: A 299 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7764 (mtmt) REVERT: A 451 ASN cc_start: 0.9039 (p0) cc_final: 0.8628 (p0) REVERT: A 478 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 603 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8621 (pp30) REVERT: A 664 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8649 (ptm160) REVERT: A 843 SER cc_start: 0.8396 (t) cc_final: 0.7919 (p) REVERT: A 847 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: A 852 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8853 (mp) REVERT: A 875 ASP cc_start: 0.8769 (m-30) cc_final: 0.8466 (m-30) REVERT: A 889 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7949 (mm-40) REVERT: A 1185 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8462 (mm-30) REVERT: A 1303 ILE cc_start: 0.8924 (pt) cc_final: 0.8700 (pp) REVERT: A 1528 LYS cc_start: 0.9252 (ttmm) cc_final: 0.8882 (ttmm) REVERT: A 1613 MET cc_start: 0.9036 (mtp) cc_final: 0.8603 (ttt) REVERT: A 1623 ASN cc_start: 0.8261 (m-40) cc_final: 0.8024 (p0) outliers start: 11 outliers final: 3 residues processed: 78 average time/residue: 0.6076 time to fit residues: 51.0617 Evaluate side-chains 80 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 664 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.0060 chunk 70 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067789 restraints weight = 21129.598| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.17 r_work: 0.2766 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12495 Z= 0.145 Angle : 0.515 9.343 17413 Z= 0.277 Chirality : 0.038 0.218 1977 Planarity : 0.003 0.031 1773 Dihedral : 18.619 130.367 3002 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.97 % Allowed : 12.36 % Favored : 86.68 % 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: 1.97 (0.25), residues: 1120 helix: 2.20 (0.23), residues: 512 sheet: 0.30 (0.38), residues: 157 loop : 0.79 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.013 0.001 TYR A1328 PHE 0.015 0.001 PHE A1419 TRP 0.011 0.001 TRP A 78 HIS 0.004 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00326 (12495) covalent geometry : angle 0.51548 (17413) hydrogen bonds : bond 0.03279 ( 536) hydrogen bonds : angle 3.63013 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.51 seconds wall clock time: 60 minutes 15.47 seconds (3615.47 seconds total)