Starting phenix.real_space_refine on Thu Jun 4 22:16:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfu_71614/06_2026/9pfu_71614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfu_71614/06_2026/9pfu_71614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pfu_71614/06_2026/9pfu_71614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfu_71614/06_2026/9pfu_71614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfu_71614/06_2026/9pfu_71614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfu_71614/06_2026/9pfu_71614.map" } resolution = 3.54 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= 0.001 sd= 0.051 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 13 5.49 5 S 83 5.16 5 C 9934 2.51 5 N 2635 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15581 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1604, 13137 Classifications: {'peptide': 1604} Link IDs: {'PTRANS': 49, 'TRANS': 1554} Chain breaks: 4 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 430 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Chain: "P" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "T" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 7} Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15581 At special positions: 0 Unit cell: (117.264, 95.277, 131.922, 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 83 16.00 P 13 15.00 O 2916 8.00 N 2635 7.00 C 9934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 715.4 milliseconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 10 sheets defined 62.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.589A pdb=" N CYS A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.252A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 4.019A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.791A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 351 through 380 removed outlier: 3.831A pdb=" N PHE A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 413 removed outlier: 4.083A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.650A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 552 " --> pdb=" O ILE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.534A pdb=" N LYS A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 714 through 725 removed outlier: 3.825A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 851 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 901 through 920 removed outlier: 3.812A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.599A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1021 removed outlier: 4.220A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 4.961A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1110 Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.894A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 3.601A pdb=" N GLU A1152 " --> pdb=" O ASN A1149 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1149 through 1153' Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 3.649A pdb=" N VAL A1280 " --> pdb=" O ASN A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 4.191A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1367 through 1373 removed outlier: 4.306A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1404 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 3.618A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1511 removed outlier: 3.633A pdb=" N ILE A1491 " --> pdb=" O HIS A1487 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A1511 " --> pdb=" O MET A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1527 Processing helix chain 'A' and resid 1530 through 1546 Processing helix chain 'A' and resid 1565 through 1570 Processing helix chain 'A' and resid 1571 through 1583 removed outlier: 3.925A pdb=" N TRP A1575 " --> pdb=" O ASP A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1595 removed outlier: 4.002A pdb=" N TYR A1590 " --> pdb=" O LYS A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1600 Processing helix chain 'A' and resid 1603 through 1617 removed outlier: 3.970A pdb=" N VAL A1617 " --> pdb=" O LYS A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1648 removed outlier: 3.710A pdb=" N ILE A1639 " --> pdb=" O HIS A1635 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A1648 " --> pdb=" O ASP A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1671 removed outlier: 3.979A pdb=" N TYR A1669 " --> pdb=" O ASN A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1696 Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.863A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 156 Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.920A pdb=" N GLY C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 172 through 200 removed outlier: 3.580A pdb=" N MET D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 removed outlier: 3.510A pdb=" N ARG E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.452A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 631 removed outlier: 3.548A pdb=" N PHE A 629 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 removed outlier: 3.659A pdb=" N GLN A 813 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 817 " --> pdb=" O CYS A 695 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.743A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1116 through 1117 Processing sheet with id=AA8, first strand: chain 'A' and resid 1231 through 1233 removed outlier: 3.578A pdb=" N ILE A1410 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A1243 " --> pdb=" O ILE A1410 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A1412 " --> pdb=" O ILE A1241 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A1241 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AB1, first strand: chain 'A' and resid 1624 through 1626 844 hydrogen bonds defined for protein. 2463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.87 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: 3058 1.33 - 1.45: 3729 1.45 - 1.57: 8948 1.57 - 1.70: 24 1.70 - 1.82: 139 Bond restraints: 15898 Sorted by residual: bond pdb=" N ASP E 164 " pdb=" CA ASP E 164 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" C SER A 870 " pdb=" N LYS A 871 " ideal model delta sigma weight residual 1.332 1.297 0.036 1.38e-02 5.25e+03 6.64e+00 bond pdb=" C LYS A 871 " pdb=" O LYS A 871 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.66e-02 3.63e+03 3.09e+00 bond pdb=" CA ASP E 190 " pdb=" CB ASP E 190 " ideal model delta sigma weight residual 1.527 1.570 -0.042 2.48e-02 1.63e+03 2.91e+00 bond pdb=" N ASN A 538 " pdb=" CA ASN A 538 " ideal model delta sigma weight residual 1.455 1.478 -0.022 1.32e-02 5.74e+03 2.84e+00 ... (remaining 15893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 21373 2.91 - 5.82: 141 5.82 - 8.73: 16 8.73 - 11.64: 6 11.64 - 14.55: 1 Bond angle restraints: 21537 Sorted by residual: angle pdb=" N LYS A 871 " pdb=" CA LYS A 871 " pdb=" CB LYS A 871 " ideal model delta sigma weight residual 112.63 104.60 8.03 1.61e+00 3.86e-01 2.49e+01 angle pdb=" CB MET A1396 " pdb=" CG MET A1396 " pdb=" SD MET A1396 " ideal model delta sigma weight residual 112.70 98.15 14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CB MET E 195 " pdb=" CG MET E 195 " pdb=" SD MET E 195 " ideal model delta sigma weight residual 112.70 123.68 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA LEU B 146 " pdb=" CB LEU B 146 " pdb=" CG LEU B 146 " ideal model delta sigma weight residual 116.30 127.74 -11.44 3.50e+00 8.16e-02 1.07e+01 ... (remaining 21532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8548 17.90 - 35.80: 915 35.80 - 53.70: 170 53.70 - 71.61: 31 71.61 - 89.51: 18 Dihedral angle restraints: 9682 sinusoidal: 4111 harmonic: 5571 Sorted by residual: dihedral pdb=" CA GLU A1584 " pdb=" C GLU A1584 " pdb=" N GLN A1585 " pdb=" CA GLN A1585 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ILE A1529 " pdb=" C ILE A1529 " pdb=" N ASN A1530 " pdb=" CA ASN A1530 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP A 865 " pdb=" C ASP A 865 " pdb=" N MET A 866 " pdb=" CA MET A 866 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2022 0.054 - 0.108: 418 0.108 - 0.162: 42 0.162 - 0.216: 8 0.216 - 0.270: 2 Chirality restraints: 2492 Sorted by residual: chirality pdb=" CA MET A 360 " pdb=" N MET A 360 " pdb=" C MET A 360 " pdb=" CB MET A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2489 not shown) Planarity restraints: 2652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 190 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" CG ASP E 190 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP E 190 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP E 190 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 682 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C ASN A 682 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 682 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 683 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1132 " -0.017 2.00e-02 2.50e+03 1.44e-02 4.13e+00 pdb=" CG TYR A1132 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A1132 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A1132 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A1132 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A1132 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1132 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1132 " 0.001 2.00e-02 2.50e+03 ... (remaining 2649 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2661 2.77 - 3.30: 15412 3.30 - 3.83: 26383 3.83 - 4.37: 30068 4.37 - 4.90: 52539 Nonbonded interactions: 127063 Sorted by model distance: nonbonded pdb=" O THR A1259 " pdb=" OG1 THR A1359 " model vdw 2.236 3.040 nonbonded pdb=" ND2 ASN A1304 " pdb=" O VAL A1431 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASN A 603 " pdb=" NZ LYS B 180 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A1376 " pdb=" O ILE A1419 " model vdw 2.260 3.040 nonbonded pdb=" O ALA A1052 " pdb=" OG1 THR A1056 " model vdw 2.263 3.040 ... (remaining 127058 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 183) selection = (chain 'C' and resid 130 through 183) } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.700 Find NCS groups from input model: 0.080 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15898 Z= 0.139 Angle : 0.657 14.547 21537 Z= 0.338 Chirality : 0.043 0.270 2492 Planarity : 0.004 0.048 2652 Dihedral : 15.156 89.507 6068 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1863 helix: 1.72 (0.15), residues: 1078 sheet: -1.08 (0.59), residues: 77 loop : -1.04 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.035 0.001 TYR A1132 PHE 0.024 0.001 PHE A1668 TRP 0.023 0.001 TRP A1610 HIS 0.004 0.001 HIS A1487 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (15898) covalent geometry : angle 0.65677 / 0.34 (21537) hydrogen bonds : bond 0.11766 / 7.38 ( 844) hydrogen bonds : angle 5.48814 / 4.01 ( 2463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.597 Fit side-chains REVERT: A 125 TYR cc_start: 0.8381 (t80) cc_final: 0.8172 (t80) REVERT: A 354 LYS cc_start: 0.7216 (mmtp) cc_final: 0.6846 (pttp) REVERT: A 851 ILE cc_start: 0.8218 (tp) cc_final: 0.8016 (tp) REVERT: A 1339 ARG cc_start: 0.7006 (mmt-90) cc_final: 0.6405 (mmm160) REVERT: A 1491 ILE cc_start: 0.8231 (mt) cc_final: 0.7996 (mt) REVERT: A 1608 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8405 (ptmt) REVERT: C 137 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8272 (mtp-110) REVERT: C 182 ARG cc_start: 0.8270 (ttm110) cc_final: 0.8051 (mtt180) REVERT: E 134 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7686 (mtm180) REVERT: E 148 MET cc_start: 0.7766 (ttm) cc_final: 0.7533 (ttm) REVERT: E 187 MET cc_start: 0.7303 (ptm) cc_final: 0.6897 (ptp) REVERT: E 195 MET cc_start: 0.7286 (mmm) cc_final: 0.6573 (mmm) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1322 time to fit residues: 71.9340 Evaluate side-chains 293 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 ASN A 705 ASN A 829 HIS A1277 ASN A1387 ASN A1536 ASN ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119213 restraints weight = 23148.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122791 restraints weight = 12168.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125188 restraints weight = 7754.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126792 restraints weight = 5628.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127864 restraints weight = 4488.839| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15898 Z= 0.138 Angle : 0.524 8.577 21537 Z= 0.276 Chirality : 0.039 0.206 2492 Planarity : 0.004 0.063 2652 Dihedral : 7.810 73.868 2253 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 10.99 % Favored : 87.85 % 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: 1.24 (0.20), residues: 1863 helix: 2.00 (0.15), residues: 1091 sheet: -0.98 (0.55), residues: 85 loop : -0.89 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 462 TYR 0.016 0.001 TYR A 917 PHE 0.019 0.001 PHE A 629 TRP 0.013 0.001 TRP A1610 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15898) covalent geometry : angle 0.52418 / 0.28 (21537) hydrogen bonds : bond 0.03589 / 2.34 ( 844) hydrogen bonds : angle 4.46714 / 3.27 ( 2463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8223 (mtm) cc_final: 0.7814 (mtm) REVERT: A 354 LYS cc_start: 0.7578 (mmtp) cc_final: 0.6837 (pttp) REVERT: A 473 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7873 (t80) REVERT: A 539 ASP cc_start: 0.8234 (t0) cc_final: 0.8010 (t0) REVERT: A 627 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6825 (ttp80) REVERT: A 673 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7712 (mm) REVERT: A 774 MET cc_start: 0.7218 (mmm) cc_final: 0.6939 (mmt) REVERT: A 851 ILE cc_start: 0.8069 (tp) cc_final: 0.7758 (tp) REVERT: A 865 ASP cc_start: 0.7816 (p0) cc_final: 0.7541 (p0) REVERT: A 1135 GLU cc_start: 0.8683 (tp30) cc_final: 0.8020 (tp30) REVERT: A 1141 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 1536 ASN cc_start: 0.7210 (m-40) cc_final: 0.6923 (m-40) REVERT: C 148 MET cc_start: 0.8177 (mtt) cc_final: 0.7934 (mtt) REVERT: C 182 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8034 (mpt-90) REVERT: E 190 ASP cc_start: 0.8246 (p0) cc_final: 0.8007 (p0) outliers start: 20 outliers final: 13 residues processed: 324 average time/residue: 0.1245 time to fit residues: 60.3260 Evaluate side-chains 310 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 171 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 ASN A 689 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN A 876 ASN A1335 ASN A1387 ASN ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112118 restraints weight = 23317.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115599 restraints weight = 12306.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117907 restraints weight = 7869.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119465 restraints weight = 5750.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120483 restraints weight = 4612.948| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15898 Z= 0.175 Angle : 0.542 7.945 21537 Z= 0.285 Chirality : 0.040 0.230 2492 Planarity : 0.004 0.048 2652 Dihedral : 7.836 73.985 2253 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.97 % Allowed : 14.05 % Favored : 83.98 % 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: 1.22 (0.20), residues: 1863 helix: 1.98 (0.15), residues: 1096 sheet: -0.74 (0.57), residues: 80 loop : -0.94 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 462 TYR 0.024 0.002 TYR A 125 PHE 0.018 0.001 PHE A 424 TRP 0.015 0.001 TRP A1610 HIS 0.032 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (15898) covalent geometry : angle 0.54157 / 0.28 (21537) hydrogen bonds : bond 0.03794 / 2.47 ( 844) hydrogen bonds : angle 4.30716 / 3.18 ( 2463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 0.624 Fit side-chains REVERT: A 59 MET cc_start: 0.8429 (mtm) cc_final: 0.8084 (mtm) REVERT: A 87 PHE cc_start: 0.8022 (m-80) cc_final: 0.7784 (m-80) REVERT: A 353 ARG cc_start: 0.8545 (ptp-170) cc_final: 0.8300 (ptp90) REVERT: A 354 LYS cc_start: 0.7706 (mmtp) cc_final: 0.6975 (pttp) REVERT: A 360 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7656 (tpp) REVERT: A 473 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7961 (t80) REVERT: A 627 ARG cc_start: 0.7395 (ttp80) cc_final: 0.6888 (ttt-90) REVERT: A 673 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7681 (mm) REVERT: A 684 TYR cc_start: 0.8074 (p90) cc_final: 0.7804 (p90) REVERT: A 851 ILE cc_start: 0.8261 (tp) cc_final: 0.7854 (tp) REVERT: A 1132 TYR cc_start: 0.8515 (t80) cc_final: 0.7878 (t80) REVERT: A 1136 LYS cc_start: 0.8496 (mttm) cc_final: 0.7997 (mttp) REVERT: A 1141 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 1278 ARG cc_start: 0.7833 (tpt170) cc_final: 0.7607 (tpt170) REVERT: A 1409 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7318 (ttm110) REVERT: A 1536 ASN cc_start: 0.7208 (m-40) cc_final: 0.6976 (m-40) REVERT: A 1669 TYR cc_start: 0.6702 (m-80) cc_final: 0.6320 (m-10) REVERT: E 145 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8010 (mt) REVERT: E 187 MET cc_start: 0.7691 (ptm) cc_final: 0.7354 (ptt) REVERT: E 190 ASP cc_start: 0.8144 (p0) cc_final: 0.7787 (p0) outliers start: 34 outliers final: 19 residues processed: 318 average time/residue: 0.1303 time to fit residues: 60.9534 Evaluate side-chains 302 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 165 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 682 ASN A 705 ASN A 766 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112188 restraints weight = 23448.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115700 restraints weight = 12474.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118028 restraints weight = 8011.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119600 restraints weight = 5882.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120594 restraints weight = 4727.007| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15898 Z= 0.134 Angle : 0.497 8.159 21537 Z= 0.262 Chirality : 0.039 0.236 2492 Planarity : 0.003 0.041 2652 Dihedral : 7.768 73.975 2253 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.26 % Allowed : 16.60 % Favored : 81.15 % 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: 1.36 (0.20), residues: 1863 helix: 2.11 (0.16), residues: 1090 sheet: -0.77 (0.60), residues: 73 loop : -0.89 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 182 TYR 0.013 0.001 TYR A1490 PHE 0.016 0.001 PHE A 629 TRP 0.013 0.001 TRP A1610 HIS 0.003 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (15898) covalent geometry : angle 0.49736 / 0.26 (21537) hydrogen bonds : bond 0.03550 / 2.32 ( 844) hydrogen bonds : angle 4.18964 / 3.09 ( 2463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 354 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7000 (pttp) REVERT: A 360 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7458 (tpp) REVERT: A 473 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7952 (t80) REVERT: A 673 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 677 ILE cc_start: 0.8976 (tt) cc_final: 0.8749 (tt) REVERT: A 684 TYR cc_start: 0.8099 (p90) cc_final: 0.7858 (p90) REVERT: A 851 ILE cc_start: 0.8328 (tp) cc_final: 0.7887 (tp) REVERT: A 906 GLU cc_start: 0.7586 (tt0) cc_final: 0.7111 (tp30) REVERT: A 1132 TYR cc_start: 0.8597 (t80) cc_final: 0.7906 (t80) REVERT: A 1136 LYS cc_start: 0.8457 (mttm) cc_final: 0.7924 (mttp) REVERT: A 1141 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 1278 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7606 (tpt170) REVERT: A 1409 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7354 (ttm110) REVERT: A 1637 LYS cc_start: 0.7856 (pttm) cc_final: 0.7335 (ttmt) REVERT: A 1669 TYR cc_start: 0.6657 (m-80) cc_final: 0.6258 (m-10) REVERT: C 137 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8336 (mtp-110) REVERT: E 187 MET cc_start: 0.7658 (ptm) cc_final: 0.7367 (ptt) REVERT: E 190 ASP cc_start: 0.8139 (p0) cc_final: 0.7878 (p0) outliers start: 39 outliers final: 25 residues processed: 310 average time/residue: 0.1292 time to fit residues: 59.3268 Evaluate side-chains 310 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 39 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 134 optimal weight: 0.0070 chunk 30 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 632 GLN A 638 GLN A 682 ASN A 705 ASN A 766 GLN A 813 GLN ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114300 restraints weight = 23260.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117829 restraints weight = 12209.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120176 restraints weight = 7762.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121764 restraints weight = 5652.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122798 restraints weight = 4511.360| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15898 Z= 0.102 Angle : 0.476 9.204 21537 Z= 0.253 Chirality : 0.038 0.247 2492 Planarity : 0.003 0.044 2652 Dihedral : 7.690 73.965 2253 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.37 % Allowed : 17.64 % Favored : 79.99 % 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: 1.49 (0.20), residues: 1863 helix: 2.21 (0.16), residues: 1088 sheet: -0.64 (0.60), residues: 78 loop : -0.82 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 182 TYR 0.023 0.001 TYR A 34 PHE 0.017 0.001 PHE A 629 TRP 0.018 0.001 TRP A 780 HIS 0.003 0.000 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (15898) covalent geometry : angle 0.47619 / 0.25 (21537) hydrogen bonds : bond 0.03310 / 2.17 ( 844) hydrogen bonds : angle 4.10358 / 3.03 ( 2463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8110 (mtm) cc_final: 0.7625 (mtm) REVERT: A 340 MET cc_start: 0.8285 (tpt) cc_final: 0.7987 (tpt) REVERT: A 354 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7042 (pttp) REVERT: A 360 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7207 (tpp) REVERT: A 473 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8018 (t80) REVERT: A 673 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7541 (mm) REVERT: A 677 ILE cc_start: 0.8957 (tt) cc_final: 0.8738 (tt) REVERT: A 684 TYR cc_start: 0.8105 (p90) cc_final: 0.7893 (p90) REVERT: A 851 ILE cc_start: 0.8260 (tp) cc_final: 0.7829 (tp) REVERT: A 906 GLU cc_start: 0.7602 (tt0) cc_final: 0.7203 (tp30) REVERT: A 936 GLN cc_start: 0.8633 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 989 ASP cc_start: 0.9319 (t0) cc_final: 0.8998 (t70) REVERT: A 1132 TYR cc_start: 0.8613 (t80) cc_final: 0.8335 (t80) REVERT: A 1141 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 1158 ASP cc_start: 0.7989 (p0) cc_final: 0.7742 (p0) REVERT: A 1409 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7363 (ttm110) REVERT: A 1536 ASN cc_start: 0.6997 (m-40) cc_final: 0.6781 (m-40) REVERT: A 1574 TYR cc_start: 0.8592 (t80) cc_final: 0.8106 (t80) REVERT: A 1586 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8302 (ptpp) REVERT: A 1637 LYS cc_start: 0.7868 (pttm) cc_final: 0.7345 (ttmt) REVERT: A 1669 TYR cc_start: 0.6657 (m-80) cc_final: 0.6248 (m-10) REVERT: C 137 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8402 (mtp-110) REVERT: E 187 MET cc_start: 0.7741 (ptm) cc_final: 0.7447 (ptt) REVERT: E 190 ASP cc_start: 0.8009 (p0) cc_final: 0.7783 (p0) REVERT: E 195 MET cc_start: 0.8220 (mmm) cc_final: 0.7357 (mtt) outliers start: 41 outliers final: 25 residues processed: 331 average time/residue: 0.1314 time to fit residues: 64.1171 Evaluate side-chains 316 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 113 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN A 766 GLN A 813 GLN ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108630 restraints weight = 23344.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112043 restraints weight = 12431.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114315 restraints weight = 8006.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115852 restraints weight = 5892.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116859 restraints weight = 4742.962| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15898 Z= 0.195 Angle : 0.559 9.103 21537 Z= 0.292 Chirality : 0.041 0.250 2492 Planarity : 0.003 0.045 2652 Dihedral : 7.839 73.921 2253 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.60 % Allowed : 19.20 % Favored : 78.20 % 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: 1.30 (0.20), residues: 1863 helix: 2.04 (0.16), residues: 1089 sheet: -0.50 (0.56), residues: 80 loop : -0.91 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 182 TYR 0.026 0.002 TYR A 211 PHE 0.018 0.001 PHE A 424 TRP 0.010 0.001 TRP A 932 HIS 0.004 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (15898) covalent geometry : angle 0.55900 / 0.29 (21537) hydrogen bonds : bond 0.03878 / 2.53 ( 844) hydrogen bonds : angle 4.22802 / 3.13 ( 2463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8303 (ttmt) REVERT: A 59 MET cc_start: 0.8171 (mtm) cc_final: 0.7652 (mtm) REVERT: A 360 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7722 (tpp) REVERT: A 473 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 673 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 684 TYR cc_start: 0.8152 (p90) cc_final: 0.7930 (p90) REVERT: A 851 ILE cc_start: 0.8457 (tp) cc_final: 0.7954 (tp) REVERT: A 906 GLU cc_start: 0.7800 (tt0) cc_final: 0.7296 (tp30) REVERT: A 981 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (mp) REVERT: A 989 ASP cc_start: 0.9374 (t0) cc_final: 0.9048 (t70) REVERT: A 1132 TYR cc_start: 0.8675 (t80) cc_final: 0.8438 (t80) REVERT: A 1141 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 1409 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7639 (ttm110) REVERT: A 1586 LYS cc_start: 0.8674 (ptpt) cc_final: 0.8373 (ptpp) REVERT: A 1637 LYS cc_start: 0.7902 (pttm) cc_final: 0.7295 (ttmt) REVERT: A 1669 TYR cc_start: 0.6655 (m-80) cc_final: 0.6323 (m-10) REVERT: C 137 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8506 (mmm-85) REVERT: E 190 ASP cc_start: 0.8122 (p0) cc_final: 0.7903 (p0) outliers start: 45 outliers final: 32 residues processed: 314 average time/residue: 0.1323 time to fit residues: 61.7123 Evaluate side-chains 308 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN A 766 GLN A1098 GLN ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109174 restraints weight = 23293.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112553 restraints weight = 12351.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114842 restraints weight = 7991.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116278 restraints weight = 5892.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117355 restraints weight = 4798.225| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15898 Z= 0.160 Angle : 0.531 9.596 21537 Z= 0.279 Chirality : 0.040 0.253 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.844 73.921 2253 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 19.95 % Favored : 77.56 % 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: 1.32 (0.20), residues: 1863 helix: 2.05 (0.15), residues: 1085 sheet: -0.35 (0.58), residues: 78 loop : -0.88 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 182 TYR 0.023 0.001 TYR A1642 PHE 0.015 0.001 PHE A 424 TRP 0.016 0.001 TRP A1610 HIS 0.005 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15898) covalent geometry : angle 0.53104 / 0.28 (21537) hydrogen bonds : bond 0.03712 / 2.43 ( 844) hydrogen bonds : angle 4.20051 / 3.11 ( 2463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8160 (mtm) cc_final: 0.7596 (mtm) REVERT: A 340 MET cc_start: 0.8413 (tpt) cc_final: 0.8044 (tpt) REVERT: A 360 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7479 (tpp) REVERT: A 473 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8016 (t80) REVERT: A 673 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 684 TYR cc_start: 0.8167 (p90) cc_final: 0.7952 (p90) REVERT: A 851 ILE cc_start: 0.8454 (tp) cc_final: 0.7953 (tp) REVERT: A 906 GLU cc_start: 0.7788 (tt0) cc_final: 0.7288 (tp30) REVERT: A 981 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 989 ASP cc_start: 0.9373 (t0) cc_final: 0.9053 (t70) REVERT: A 1132 TYR cc_start: 0.8647 (t80) cc_final: 0.8446 (t80) REVERT: A 1141 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 1409 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7479 (ttm110) REVERT: A 1586 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8422 (ptpp) REVERT: A 1637 LYS cc_start: 0.7788 (pttm) cc_final: 0.7287 (ttmt) REVERT: A 1669 TYR cc_start: 0.6662 (m-80) cc_final: 0.6389 (m-10) REVERT: C 137 ARG cc_start: 0.8729 (mmm-85) cc_final: 0.8504 (mmm-85) outliers start: 43 outliers final: 31 residues processed: 310 average time/residue: 0.1290 time to fit residues: 59.4316 Evaluate side-chains 309 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN A 766 GLN ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109761 restraints weight = 23287.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113211 restraints weight = 12302.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115517 restraints weight = 7875.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117071 restraints weight = 5761.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118075 restraints weight = 4628.937| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15898 Z= 0.144 Angle : 0.526 9.817 21537 Z= 0.277 Chirality : 0.040 0.267 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.830 73.932 2253 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.95 % Allowed : 19.78 % Favored : 77.27 % 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: 1.34 (0.20), residues: 1863 helix: 2.05 (0.15), residues: 1087 sheet: -0.23 (0.57), residues: 80 loop : -0.87 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 182 TYR 0.032 0.001 TYR A 34 PHE 0.014 0.001 PHE A 424 TRP 0.016 0.001 TRP A1610 HIS 0.005 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (15898) covalent geometry : angle 0.52617 / 0.28 (21537) hydrogen bonds : bond 0.03635 / 2.39 ( 844) hydrogen bonds : angle 4.18135 / 3.10 ( 2463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8295 (ptpt) REVERT: A 59 MET cc_start: 0.8176 (mtm) cc_final: 0.7660 (mtm) REVERT: A 360 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7167 (tpp) REVERT: A 421 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 473 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8046 (t80) REVERT: A 673 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7633 (mm) REVERT: A 677 ILE cc_start: 0.8992 (tt) cc_final: 0.8730 (tt) REVERT: A 684 TYR cc_start: 0.8173 (p90) cc_final: 0.7966 (p90) REVERT: A 851 ILE cc_start: 0.8445 (tp) cc_final: 0.7953 (tp) REVERT: A 906 GLU cc_start: 0.7801 (tt0) cc_final: 0.7316 (tp30) REVERT: A 981 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 989 ASP cc_start: 0.9358 (t0) cc_final: 0.9039 (t70) REVERT: A 1132 TYR cc_start: 0.8624 (t80) cc_final: 0.7960 (t80) REVERT: A 1136 LYS cc_start: 0.8558 (mttm) cc_final: 0.8013 (mttm) REVERT: A 1141 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 1409 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7418 (ttm110) REVERT: A 1586 LYS cc_start: 0.8719 (ptpt) cc_final: 0.8367 (ptpp) REVERT: A 1610 TRP cc_start: 0.8529 (t60) cc_final: 0.8288 (t60) REVERT: A 1637 LYS cc_start: 0.7895 (pttm) cc_final: 0.7374 (ttmt) REVERT: A 1669 TYR cc_start: 0.6588 (m-80) cc_final: 0.6371 (m-10) REVERT: C 137 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8429 (mtp-110) outliers start: 51 outliers final: 36 residues processed: 319 average time/residue: 0.1249 time to fit residues: 59.9514 Evaluate side-chains 321 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 155 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN A 876 ASN A1022 HIS ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110928 restraints weight = 23119.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114375 restraints weight = 12180.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116694 restraints weight = 7801.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118251 restraints weight = 5702.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119256 restraints weight = 4580.159| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15898 Z= 0.130 Angle : 0.532 9.890 21537 Z= 0.276 Chirality : 0.040 0.284 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.801 73.919 2253 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.72 % Allowed : 20.13 % Favored : 77.15 % 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: 1.42 (0.20), residues: 1863 helix: 2.10 (0.16), residues: 1082 sheet: -0.11 (0.59), residues: 78 loop : -0.81 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 182 TYR 0.029 0.001 TYR A1642 PHE 0.013 0.001 PHE A 424 TRP 0.015 0.001 TRP A1610 HIS 0.006 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15898) covalent geometry : angle 0.53199 / 0.28 (21537) hydrogen bonds : bond 0.03510 / 2.30 ( 844) hydrogen bonds : angle 4.15046 / 3.07 ( 2463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8266 (ptpt) REVERT: A 59 MET cc_start: 0.8185 (mtm) cc_final: 0.7687 (mtm) REVERT: A 360 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: A 421 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 473 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 673 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 677 ILE cc_start: 0.8958 (tt) cc_final: 0.8703 (tt) REVERT: A 684 TYR cc_start: 0.8168 (p90) cc_final: 0.7965 (p90) REVERT: A 774 MET cc_start: 0.7453 (mmm) cc_final: 0.7115 (mmt) REVERT: A 851 ILE cc_start: 0.8326 (tp) cc_final: 0.7807 (tp) REVERT: A 906 GLU cc_start: 0.7779 (tt0) cc_final: 0.7298 (tp30) REVERT: A 936 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 981 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 1132 TYR cc_start: 0.8606 (t80) cc_final: 0.7925 (t80) REVERT: A 1136 LYS cc_start: 0.8516 (mttm) cc_final: 0.7950 (mttm) REVERT: A 1141 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 1361 TYR cc_start: 0.8558 (m-80) cc_final: 0.7708 (m-80) REVERT: A 1409 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7391 (ttm110) REVERT: A 1610 TRP cc_start: 0.8523 (t60) cc_final: 0.8283 (t60) REVERT: A 1637 LYS cc_start: 0.7904 (pttm) cc_final: 0.7340 (ttmt) REVERT: B 180 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7230 (tttm) REVERT: C 137 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8264 (mtp85) REVERT: C 182 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7521 (mtm-85) REVERT: E 134 ARG cc_start: 0.8371 (mtm180) cc_final: 0.8099 (mtm180) outliers start: 47 outliers final: 35 residues processed: 312 average time/residue: 0.1282 time to fit residues: 59.5944 Evaluate side-chains 318 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 44 optimal weight: 0.0050 chunk 135 optimal weight: 5.9990 chunk 35 optimal weight: 0.0470 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN A1098 GLN ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112742 restraints weight = 23074.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116187 restraints weight = 12057.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118517 restraints weight = 7696.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120091 restraints weight = 5613.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121056 restraints weight = 4500.822| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15898 Z= 0.112 Angle : 0.530 10.086 21537 Z= 0.276 Chirality : 0.040 0.432 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.748 73.911 2253 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.37 % Allowed : 20.59 % Favored : 77.04 % 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: 1.49 (0.20), residues: 1863 helix: 2.15 (0.16), residues: 1081 sheet: -0.10 (0.60), residues: 78 loop : -0.76 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 182 TYR 0.032 0.001 TYR A1642 PHE 0.013 0.001 PHE A1668 TRP 0.015 0.001 TRP A1610 HIS 0.006 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15898) covalent geometry : angle 0.53005 / 0.28 (21537) hydrogen bonds : bond 0.03351 / 2.19 ( 844) hydrogen bonds : angle 4.11679 / 3.04 ( 2463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8179 (ptpt) REVERT: A 59 MET cc_start: 0.8153 (mtm) cc_final: 0.7686 (mtm) REVERT: A 360 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: A 421 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 440 MET cc_start: 0.8318 (tpp) cc_final: 0.8097 (tpp) REVERT: A 473 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 673 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7539 (mm) REVERT: A 677 ILE cc_start: 0.8926 (tt) cc_final: 0.8681 (tt) REVERT: A 684 TYR cc_start: 0.8151 (p90) cc_final: 0.7940 (p90) REVERT: A 774 MET cc_start: 0.7465 (mmm) cc_final: 0.7140 (mmt) REVERT: A 851 ILE cc_start: 0.8226 (tp) cc_final: 0.7754 (tp) REVERT: A 906 GLU cc_start: 0.7756 (tt0) cc_final: 0.7290 (tp30) REVERT: A 936 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 1132 TYR cc_start: 0.8567 (t80) cc_final: 0.7867 (t80) REVERT: A 1136 LYS cc_start: 0.8509 (mttm) cc_final: 0.7913 (mttm) REVERT: A 1141 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 1361 TYR cc_start: 0.8511 (m-80) cc_final: 0.7514 (m-80) REVERT: A 1409 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7345 (ttm110) REVERT: A 1415 LYS cc_start: 0.7367 (mmmt) cc_final: 0.7081 (mmtt) REVERT: A 1442 LYS cc_start: 0.8881 (mttt) cc_final: 0.8629 (mtpt) REVERT: A 1574 TYR cc_start: 0.8697 (t80) cc_final: 0.8324 (t80) REVERT: A 1610 TRP cc_start: 0.8501 (t60) cc_final: 0.8291 (t60) REVERT: A 1637 LYS cc_start: 0.7840 (pttm) cc_final: 0.7324 (ttmt) REVERT: A 1674 PHE cc_start: 0.7866 (m-80) cc_final: 0.7501 (m-80) REVERT: B 180 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7222 (tttm) REVERT: C 137 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8268 (mtp85) REVERT: C 182 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7542 (mtm-85) REVERT: E 134 ARG cc_start: 0.8389 (mtm180) cc_final: 0.7960 (mtm180) outliers start: 41 outliers final: 32 residues processed: 315 average time/residue: 0.1259 time to fit residues: 59.3091 Evaluate side-chains 322 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110033 restraints weight = 23236.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113420 restraints weight = 12299.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115726 restraints weight = 7902.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117252 restraints weight = 5777.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118281 restraints weight = 4656.718| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15898 Z= 0.162 Angle : 0.559 9.858 21537 Z= 0.288 Chirality : 0.041 0.355 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.811 73.881 2253 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.43 % Allowed : 20.88 % Favored : 76.69 % 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: 1.40 (0.20), residues: 1863 helix: 2.07 (0.16), residues: 1081 sheet: -0.07 (0.60), residues: 78 loop : -0.79 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 182 TYR 0.031 0.001 TYR A1642 PHE 0.015 0.001 PHE A 424 TRP 0.013 0.001 TRP A1610 HIS 0.004 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (15898) covalent geometry : angle 0.55880 / 0.29 (21537) hydrogen bonds : bond 0.03596 / 2.35 ( 844) hydrogen bonds : angle 4.17074 / 3.09 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.32 seconds wall clock time: 47 minutes 45.11 seconds (2865.11 seconds total)