Starting phenix.real_space_refine on Thu Aug 6 15:34:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfu_71614/08_2026/9pfu_71614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfu_71614/08_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_71614/08_2026/9pfu_71614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfu_71614/08_2026/9pfu_71614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfu_71614/08_2026/9pfu_71614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfu_71614/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 3.32, per 1000 atoms: 0.21 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: 1.33 Conformation dependent library (CDL) restraints added in 791.3 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: 0.61 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: 3.39 Time building geometry restraints manager: 1.79 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: 2009 0.054 - 0.108: 420 0.108 - 0.162: 53 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: 0.620 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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= 0.140 Angle : 0.664 14.547 21537 Z= 0.349 Chirality : 0.044 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 0.66381 / 0.35 (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 : 0.574 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: 0.1370 time to fit residues: 75.1171 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 : 0.599 ------------------------------------------------------------------------------- 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... 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 = 0.3661 r_free = 0.3661 target = 0.143354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120671 restraints weight = 23125.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124263 restraints weight = 12066.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126682 restraints weight = 7642.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128271 restraints weight = 5541.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129378 restraints weight = 4416.931| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15898 Z= 0.143 Angle : 0.542 10.700 21537 Z= 0.285 Chirality : 0.039 0.201 2492 Planarity : 0.004 0.057 2652 Dihedral : 7.824 73.922 2253 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.16 % Allowed : 10.76 % Favored : 88.09 % 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: 1.16 (0.19), residues: 1863 helix: 1.92 (0.15), residues: 1093 sheet: -0.93 (0.57), residues: 80 loop : -0.92 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1409 TYR 0.016 0.001 TYR A 917 PHE 0.022 0.001 PHE A 629 TRP 0.013 0.001 TRP A1610 HIS 0.004 0.001 HIS A 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15898) covalent geometry : angle 0.54168 / 0.28 (21537) hydrogen bonds : bond 0.03700 / 2.39 ( 844) hydrogen bonds : angle 4.59257 / 3.37 ( 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 333 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 313 time to evaluate : 0.652 Fit side-chains REVERT: A 59 MET cc_start: 0.8233 (mtm) cc_final: 0.7834 (mtm) REVERT: A 354 LYS cc_start: 0.7514 (mmtp) cc_final: 0.6753 (pttp) REVERT: A 473 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7740 (t80) REVERT: A 539 ASP cc_start: 0.8161 (t0) cc_final: 0.7875 (t0) REVERT: A 774 MET cc_start: 0.6906 (mmm) cc_final: 0.6648 (mmt) REVERT: A 851 ILE cc_start: 0.8008 (tp) cc_final: 0.7705 (tp) REVERT: A 865 ASP cc_start: 0.7869 (p0) cc_final: 0.7572 (p0) REVERT: A 1135 GLU cc_start: 0.8684 (tp30) cc_final: 0.8039 (tp30) REVERT: A 1141 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 1536 ASN cc_start: 0.7219 (m-40) cc_final: 0.6949 (m-40) REVERT: C 182 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8046 (mpt-90) outliers start: 20 outliers final: 11 residues processed: 321 average time/residue: 0.1294 time to fit residues: 62.5904 Evaluate side-chains 301 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 288 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 D residue 146 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: 4.9990 chunk 74 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN A 705 ASN A 829 HIS A 876 ASN A1635 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118408 restraints weight = 23493.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121968 restraints weight = 12325.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124380 restraints weight = 7861.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.125947 restraints weight = 5722.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127027 restraints weight = 4582.356| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15898 Z= 0.129 Angle : 0.503 7.992 21537 Z= 0.265 Chirality : 0.039 0.210 2492 Planarity : 0.003 0.045 2652 Dihedral : 7.765 73.974 2253 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 13.59 % Favored : 84.79 % 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: 1.31 (0.20), residues: 1863 helix: 2.08 (0.16), residues: 1090 sheet: -0.98 (0.56), residues: 85 loop : -0.90 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1409 TYR 0.019 0.001 TYR A 34 PHE 0.015 0.001 PHE A1668 TRP 0.013 0.001 TRP A1610 HIS 0.006 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15898) covalent geometry : angle 0.50272 / 0.27 (21537) hydrogen bonds : bond 0.03527 / 2.29 ( 844) hydrogen bonds : angle 4.38071 / 3.22 ( 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 332 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 0.522 Fit side-chains REVERT: A 59 MET cc_start: 0.8278 (mtm) cc_final: 0.7886 (mtm) REVERT: A 87 PHE cc_start: 0.7963 (m-80) cc_final: 0.7632 (m-80) REVERT: A 354 LYS cc_start: 0.7523 (mmtp) cc_final: 0.6796 (pttp) REVERT: A 473 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7834 (t80) REVERT: A 511 ARG cc_start: 0.7225 (mtp180) cc_final: 0.6959 (mtp85) REVERT: A 539 ASP cc_start: 0.8198 (t0) cc_final: 0.7868 (t0) REVERT: A 778 GLU cc_start: 0.7273 (mp0) cc_final: 0.6995 (mp0) REVERT: A 834 TYR cc_start: 0.7857 (m-80) cc_final: 0.7523 (m-80) REVERT: A 851 ILE cc_start: 0.8057 (tp) cc_final: 0.7734 (tp) REVERT: A 865 ASP cc_start: 0.7995 (p0) cc_final: 0.7719 (p0) REVERT: A 1135 GLU cc_start: 0.8714 (tp30) cc_final: 0.7942 (tp30) REVERT: A 1141 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 1536 ASN cc_start: 0.7284 (m-40) cc_final: 0.7004 (m-40) REVERT: A 1669 TYR cc_start: 0.6829 (m-80) cc_final: 0.6462 (m-10) outliers start: 28 outliers final: 17 residues processed: 315 average time/residue: 0.1232 time to fit residues: 58.9165 Evaluate side-chains 310 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 494 LEU Chi-restraints excluded: chain A residue 705 ASN 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 1635 HIS Chi-restraints excluded: chain B residue 146 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 156 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 177 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN A 689 ASN A 705 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117352 restraints weight = 23212.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120861 restraints weight = 12103.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123237 restraints weight = 7673.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124834 restraints weight = 5563.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125873 restraints weight = 4440.527| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1635 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= 0.124 Angle : 0.489 8.481 21537 Z= 0.260 Chirality : 0.039 0.233 2492 Planarity : 0.003 0.038 2652 Dihedral : 7.727 73.972 2253 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.56 % Allowed : 14.40 % Favored : 84.04 % 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: 1.38 (0.20), residues: 1863 helix: 2.11 (0.16), residues: 1096 sheet: -0.87 (0.58), residues: 85 loop : -0.86 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1409 TYR 0.022 0.001 TYR A 34 PHE 0.015 0.001 PHE A 629 TRP 0.011 0.001 TRP A1610 HIS 0.007 0.001 HIS A1635 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (15898) covalent geometry : angle 0.48948 / 0.26 (21537) hydrogen bonds : bond 0.03415 / 2.22 ( 844) hydrogen bonds : angle 4.26200 / 3.14 ( 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 332 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 0.659 Fit side-chains REVERT: A 59 MET cc_start: 0.8424 (mtm) cc_final: 0.8084 (mtm) REVERT: A 87 PHE cc_start: 0.7918 (m-80) cc_final: 0.7679 (m-80) REVERT: A 340 MET cc_start: 0.8502 (tpt) cc_final: 0.8069 (tpt) REVERT: A 354 LYS cc_start: 0.7602 (mmtp) cc_final: 0.6879 (pttp) REVERT: A 360 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7096 (tpp) REVERT: A 473 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 511 ARG cc_start: 0.7256 (mtp180) cc_final: 0.6921 (mtp85) REVERT: A 851 ILE cc_start: 0.8094 (tp) cc_final: 0.7738 (tp) REVERT: A 865 ASP cc_start: 0.7886 (p0) cc_final: 0.7667 (p0) REVERT: A 1141 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 1536 ASN cc_start: 0.7308 (m-40) cc_final: 0.7025 (m-40) REVERT: A 1574 TYR cc_start: 0.8331 (t80) cc_final: 0.8029 (t80) REVERT: A 1586 LYS cc_start: 0.8653 (ptpt) cc_final: 0.8302 (ptpp) REVERT: A 1636 MET cc_start: 0.7696 (tpp) cc_final: 0.7353 (tpp) REVERT: A 1637 LYS cc_start: 0.7789 (pttm) cc_final: 0.7374 (ttmt) REVERT: A 1669 TYR cc_start: 0.6638 (m-80) cc_final: 0.6151 (m-10) REVERT: C 182 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7198 (mmm160) REVERT: E 187 MET cc_start: 0.7735 (ptm) cc_final: 0.7308 (ptp) REVERT: E 190 ASP cc_start: 0.8220 (p0) cc_final: 0.7856 (p0) outliers start: 27 outliers final: 16 residues processed: 319 average time/residue: 0.1307 time to fit residues: 62.1896 Evaluate side-chains 310 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 494 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 625 VAL 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 1524 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain C residue 142 LEU 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: 3.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN A 609 ASN A 682 ASN A 705 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117437 restraints weight = 23158.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120971 restraints weight = 11999.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123339 restraints weight = 7579.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124925 restraints weight = 5473.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125990 restraints weight = 4345.039| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15898 Z= 0.109 Angle : 0.476 7.759 21537 Z= 0.253 Chirality : 0.038 0.246 2492 Planarity : 0.004 0.097 2652 Dihedral : 7.690 73.956 2253 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 15.33 % Favored : 82.82 % 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: 1.43 (0.20), residues: 1863 helix: 2.16 (0.16), residues: 1096 sheet: -0.74 (0.59), residues: 83 loop : -0.87 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 822 TYR 0.017 0.001 TYR A 211 PHE 0.015 0.001 PHE A 629 TRP 0.011 0.001 TRP A1610 HIS 0.008 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15898) covalent geometry : angle 0.47552 / 0.25 (21537) hydrogen bonds : bond 0.03360 / 2.20 ( 844) hydrogen bonds : angle 4.18759 / 3.09 ( 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 334 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8379 (mtm) cc_final: 0.8021 (mtm) REVERT: A 87 PHE cc_start: 0.7868 (m-80) cc_final: 0.7626 (m-80) REVERT: A 354 LYS cc_start: 0.7607 (mmtp) cc_final: 0.6899 (pttp) REVERT: A 360 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7188 (tpp) REVERT: A 473 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 539 ASP cc_start: 0.8243 (t0) cc_final: 0.7938 (t0) REVERT: A 677 ILE cc_start: 0.8960 (tt) cc_final: 0.8719 (tt) REVERT: A 774 MET cc_start: 0.7029 (mmm) cc_final: 0.6767 (mmt) REVERT: A 851 ILE cc_start: 0.8094 (tp) cc_final: 0.7769 (tp) REVERT: A 1136 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8310 (mttm) REVERT: A 1141 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 1586 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8449 (ptpp) REVERT: A 1636 MET cc_start: 0.7732 (tpp) cc_final: 0.7410 (tpp) REVERT: A 1637 LYS cc_start: 0.7842 (pttm) cc_final: 0.7425 (ttmt) REVERT: A 1669 TYR cc_start: 0.6696 (m-80) cc_final: 0.6152 (m-10) REVERT: C 137 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8224 (mtp-110) REVERT: C 182 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7320 (mtm-85) REVERT: E 187 MET cc_start: 0.7778 (ptm) cc_final: 0.7498 (ptt) REVERT: E 190 ASP cc_start: 0.8139 (p0) cc_final: 0.7746 (p0) outliers start: 32 outliers final: 21 residues processed: 322 average time/residue: 0.1303 time to fit residues: 62.5892 Evaluate side-chains 311 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 ARG 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 142 LEU 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: 6.9990 chunk 95 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 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: 0.5980 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 705 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.138760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115831 restraints weight = 23126.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119339 restraints weight = 12111.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121687 restraints weight = 7710.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123238 restraints weight = 5613.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124289 restraints weight = 4500.277| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1945 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= 0.117 Angle : 0.482 7.634 21537 Z= 0.255 Chirality : 0.038 0.253 2492 Planarity : 0.003 0.036 2652 Dihedral : 7.658 73.916 2253 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 16.25 % Favored : 81.26 % 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: 1.44 (0.20), residues: 1863 helix: 2.15 (0.16), residues: 1097 sheet: -0.66 (0.58), residues: 83 loop : -0.86 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 709 TYR 0.030 0.001 TYR A 34 PHE 0.014 0.001 PHE A 629 TRP 0.010 0.001 TRP A1610 HIS 0.004 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15898) covalent geometry : angle 0.48206 / 0.26 (21537) hydrogen bonds : bond 0.03364 / 2.20 ( 844) hydrogen bonds : angle 4.13315 / 3.05 ( 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 344 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 301 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8345 (mtm) cc_final: 0.7958 (mtm) REVERT: A 87 PHE cc_start: 0.7883 (m-80) cc_final: 0.7659 (m-80) REVERT: A 354 LYS cc_start: 0.7661 (mmtp) cc_final: 0.6948 (pttp) REVERT: A 360 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7265 (tpp) REVERT: A 473 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 677 ILE cc_start: 0.8955 (tt) cc_final: 0.8713 (tt) REVERT: A 851 ILE cc_start: 0.8136 (tp) cc_final: 0.7788 (tp) REVERT: A 866 MET cc_start: 0.8188 (ptm) cc_final: 0.7971 (ptm) REVERT: A 906 GLU cc_start: 0.7503 (tt0) cc_final: 0.7080 (tp30) REVERT: A 1141 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 1409 ARG cc_start: 0.7358 (ttm110) cc_final: 0.7047 (ttm-80) REVERT: A 1536 ASN cc_start: 0.6908 (m-40) cc_final: 0.6630 (t0) REVERT: A 1574 TYR cc_start: 0.8468 (t80) cc_final: 0.7959 (t80) REVERT: A 1586 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8456 (ptpp) REVERT: A 1636 MET cc_start: 0.7606 (tpp) cc_final: 0.7292 (tpp) REVERT: A 1637 LYS cc_start: 0.7831 (pttm) cc_final: 0.7410 (ttmt) REVERT: A 1669 TYR cc_start: 0.6677 (m-80) cc_final: 0.6066 (m-10) REVERT: C 137 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8212 (mtp85) REVERT: C 182 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7261 (mtm-85) REVERT: E 187 MET cc_start: 0.7766 (ptm) cc_final: 0.7480 (ptt) REVERT: E 190 ASP cc_start: 0.8104 (p0) cc_final: 0.7783 (p0) outliers start: 43 outliers final: 27 residues processed: 326 average time/residue: 0.1169 time to fit residues: 56.8426 Evaluate side-chains 318 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER 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 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 ARG 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 1381 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 142 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 682 ASN A 689 ASN A 705 ASN A 766 GLN A1335 ASN ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1685 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107350 restraints weight = 23248.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110690 restraints weight = 12429.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112934 restraints weight = 8012.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114422 restraints weight = 5889.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115444 restraints weight = 4760.515| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15898 Z= 0.267 Angle : 0.648 9.181 21537 Z= 0.334 Chirality : 0.044 0.289 2492 Planarity : 0.004 0.050 2652 Dihedral : 7.892 73.942 2253 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.24 % Allowed : 17.00 % Favored : 79.76 % 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: 1.03 (0.19), residues: 1863 helix: 1.85 (0.15), residues: 1091 sheet: -0.91 (0.54), residues: 80 loop : -1.03 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 511 TYR 0.026 0.002 TYR A1361 PHE 0.027 0.002 PHE A 424 TRP 0.017 0.002 TRP A 780 HIS 0.009 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 (15898) covalent geometry : angle 0.64847 / 0.33 (21537) hydrogen bonds : bond 0.04303 / 2.80 ( 844) hydrogen bonds : angle 4.36979 / 3.24 ( 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 333 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8388 (mtm) cc_final: 0.7941 (mtm) REVERT: A 87 PHE cc_start: 0.8076 (m-80) cc_final: 0.7832 (m-80) REVERT: A 354 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7036 (pttp) REVERT: A 360 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7832 (tpp) REVERT: A 473 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7997 (t80) REVERT: A 684 TYR cc_start: 0.8177 (p90) cc_final: 0.7878 (p90) REVERT: A 851 ILE cc_start: 0.8528 (tp) cc_final: 0.8042 (tp) REVERT: A 866 MET cc_start: 0.8310 (ptm) cc_final: 0.8077 (ptm) REVERT: A 906 GLU cc_start: 0.7697 (tt0) cc_final: 0.7249 (tp30) REVERT: A 981 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8135 (mp) REVERT: A 1136 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8397 (mttm) REVERT: A 1141 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 1586 LYS cc_start: 0.8738 (ptpt) cc_final: 0.8525 (ptpp) REVERT: A 1636 MET cc_start: 0.7793 (tpp) cc_final: 0.7564 (tpp) REVERT: A 1637 LYS cc_start: 0.7957 (pttm) cc_final: 0.7404 (ttmt) REVERT: A 1669 TYR cc_start: 0.6623 (m-80) cc_final: 0.6288 (m-10) REVERT: C 137 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8260 (mtp85) REVERT: C 182 ARG cc_start: 0.7806 (tpp80) cc_final: 0.7281 (mtm-85) REVERT: E 145 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8041 (mt) REVERT: E 190 ASP cc_start: 0.8150 (p0) cc_final: 0.7840 (p0) outliers start: 56 outliers final: 40 residues processed: 306 average time/residue: 0.1238 time to fit residues: 56.8030 Evaluate side-chains 306 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 VAL 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 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 571 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 674 LYS 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 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1673 LEU 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 142 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ASP 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: 2.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109484 restraints weight = 23389.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112884 restraints weight = 12404.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115180 restraints weight = 7994.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116664 restraints weight = 5857.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117731 restraints weight = 4732.019| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 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 = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15898 Z= 0.165 Angle : 0.553 9.143 21537 Z= 0.288 Chirality : 0.041 0.249 2492 Planarity : 0.003 0.050 2652 Dihedral : 7.872 74.020 2253 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.60 % Allowed : 18.80 % Favored : 78.60 % 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: 1.15 (0.19), residues: 1863 helix: 1.95 (0.15), residues: 1093 sheet: -0.84 (0.54), residues: 80 loop : -1.01 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 511 TYR 0.024 0.002 TYR A1376 PHE 0.016 0.001 PHE A 629 TRP 0.016 0.002 TRP A1610 HIS 0.005 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (15898) covalent geometry : angle 0.55261 / 0.29 (21537) hydrogen bonds : bond 0.03903 / 2.55 ( 844) hydrogen bonds : angle 4.25600 / 3.15 ( 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 323 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8398 (mtm) cc_final: 0.7914 (mtm) REVERT: A 87 PHE cc_start: 0.7965 (m-80) cc_final: 0.7671 (m-80) REVERT: A 354 LYS cc_start: 0.7717 (mmtp) cc_final: 0.7003 (pttp) REVERT: A 360 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7625 (tpp) REVERT: A 473 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7941 (t80) REVERT: A 499 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7213 (pp) REVERT: A 684 TYR cc_start: 0.8179 (p90) cc_final: 0.7890 (p90) REVERT: A 851 ILE cc_start: 0.8482 (tp) cc_final: 0.8002 (tp) REVERT: A 906 GLU cc_start: 0.7767 (tt0) cc_final: 0.7275 (tp30) REVERT: A 989 ASP cc_start: 0.9386 (t0) cc_final: 0.9064 (t70) REVERT: A 1141 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 1361 TYR cc_start: 0.8300 (m-80) cc_final: 0.8065 (m-80) REVERT: A 1409 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7334 (ttm110) REVERT: A 1586 LYS cc_start: 0.8715 (ptpt) cc_final: 0.8293 (ptpp) REVERT: A 1636 MET cc_start: 0.7804 (tpp) cc_final: 0.7555 (tpp) REVERT: A 1637 LYS cc_start: 0.7932 (pttm) cc_final: 0.7355 (ttmt) REVERT: A 1669 TYR cc_start: 0.6624 (m-80) cc_final: 0.6249 (m-10) REVERT: C 137 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8224 (mtp85) REVERT: C 182 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7261 (mtm-85) REVERT: E 190 ASP cc_start: 0.8139 (p0) cc_final: 0.7885 (p0) outliers start: 45 outliers final: 33 residues processed: 306 average time/residue: 0.1169 time to fit residues: 54.0163 Evaluate side-chains 303 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 185 ILE 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 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 499 LEU 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 674 LYS Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR 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 1524 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain C residue 142 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 682 ASN A 705 ASN ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110868 restraints weight = 23071.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114282 restraints weight = 12122.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116577 restraints weight = 7764.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118123 restraints weight = 5676.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119077 restraints weight = 4554.878| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 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 = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15898 Z= 0.131 Angle : 0.537 9.639 21537 Z= 0.280 Chirality : 0.040 0.271 2492 Planarity : 0.003 0.050 2652 Dihedral : 7.827 74.035 2253 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 19.84 % Favored : 77.96 % 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: 1.29 (0.20), residues: 1863 helix: 2.07 (0.16), residues: 1082 sheet: -0.65 (0.56), residues: 80 loop : -0.92 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 683 TYR 0.020 0.001 TYR A 34 PHE 0.014 0.001 PHE A 629 TRP 0.018 0.002 TRP A 780 HIS 0.004 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15898) covalent geometry : angle 0.53741 / 0.28 (21537) hydrogen bonds : bond 0.03682 / 2.41 ( 844) hydrogen bonds : angle 4.19099 / 3.10 ( 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 318 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8384 (mtm) cc_final: 0.7907 (mtm) REVERT: A 87 PHE cc_start: 0.7845 (m-80) cc_final: 0.7615 (m-80) REVERT: A 360 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7441 (tpp) REVERT: A 473 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 499 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7129 (pp) REVERT: A 677 ILE cc_start: 0.8956 (tt) cc_final: 0.8693 (tt) REVERT: A 851 ILE cc_start: 0.8355 (tp) cc_final: 0.7832 (tp) REVERT: A 906 GLU cc_start: 0.7708 (tt0) cc_final: 0.7251 (tp30) REVERT: A 989 ASP cc_start: 0.9363 (t0) cc_final: 0.9049 (t70) REVERT: A 1136 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8269 (mttm) REVERT: A 1141 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 1158 ASP cc_start: 0.7848 (p0) cc_final: 0.7636 (p0) REVERT: A 1169 MET cc_start: 0.7756 (mtm) cc_final: 0.7407 (mtm) REVERT: A 1409 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7287 (ttm110) REVERT: A 1415 LYS cc_start: 0.7391 (mmmt) cc_final: 0.7107 (mmtt) REVERT: A 1586 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8562 (ptpp) REVERT: A 1636 MET cc_start: 0.7810 (tpp) cc_final: 0.7568 (tpp) REVERT: A 1637 LYS cc_start: 0.7941 (pttm) cc_final: 0.7391 (ttmt) REVERT: A 1669 TYR cc_start: 0.6592 (m-80) cc_final: 0.6228 (m-10) REVERT: C 137 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8153 (mtp85) REVERT: C 182 ARG cc_start: 0.7714 (tpp80) cc_final: 0.7231 (mtm-85) REVERT: E 190 ASP cc_start: 0.8145 (p0) cc_final: 0.7898 (p0) outliers start: 38 outliers final: 30 residues processed: 303 average time/residue: 0.1206 time to fit residues: 55.5123 Evaluate side-chains 310 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 185 ILE 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 473 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU 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 674 LYS Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1044 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 1524 THR 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 C residue 142 LEU 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=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: 2.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 44 optimal weight: 0.0050 chunk 135 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN A 682 ASN A 705 ASN A 876 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113276 restraints weight = 23169.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116748 restraints weight = 12178.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119095 restraints weight = 7768.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120656 restraints weight = 5662.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121727 restraints weight = 4544.701| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 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 = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15898 Z= 0.111 Angle : 0.519 12.707 21537 Z= 0.270 Chirality : 0.039 0.280 2492 Planarity : 0.003 0.049 2652 Dihedral : 7.735 74.010 2253 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.97 % Allowed : 19.84 % 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: 1.41 (0.20), residues: 1863 helix: 2.14 (0.16), residues: 1081 sheet: -0.40 (0.57), residues: 80 loop : -0.85 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 511 TYR 0.024 0.001 TYR A1642 PHE 0.013 0.001 PHE A 629 TRP 0.018 0.001 TRP A1610 HIS 0.006 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15898) covalent geometry : angle 0.51942 / 0.27 (21537) hydrogen bonds : bond 0.03403 / 2.22 ( 844) hydrogen bonds : angle 4.13183 / 3.06 ( 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 320 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8466 (mtm) cc_final: 0.7939 (mtm) REVERT: A 360 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6962 (tpp) REVERT: A 440 MET cc_start: 0.8322 (tpp) cc_final: 0.8112 (tpp) REVERT: A 473 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7994 (t80) REVERT: A 499 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7060 (pp) REVERT: A 677 ILE cc_start: 0.8916 (tt) cc_final: 0.8653 (tt) REVERT: A 851 ILE cc_start: 0.8317 (tp) cc_final: 0.7852 (tp) REVERT: A 906 GLU cc_start: 0.7678 (tt0) cc_final: 0.7238 (tp30) REVERT: A 936 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 979 MET cc_start: 0.8731 (tpp) cc_final: 0.8279 (mmm) REVERT: A 989 ASP cc_start: 0.9313 (t0) cc_final: 0.9017 (t70) REVERT: A 1136 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8258 (mttm) REVERT: A 1141 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8369 (mp) REVERT: A 1169 MET cc_start: 0.7747 (mtm) cc_final: 0.7483 (mtm) REVERT: A 1361 TYR cc_start: 0.8139 (m-80) cc_final: 0.7915 (m-80) REVERT: A 1409 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7266 (ttm110) REVERT: A 1415 LYS cc_start: 0.7382 (mmmt) cc_final: 0.7083 (mmtt) REVERT: A 1574 TYR cc_start: 0.8704 (t80) cc_final: 0.8246 (t80) REVERT: A 1586 LYS cc_start: 0.8806 (ptpt) cc_final: 0.8494 (ptpp) REVERT: A 1610 TRP cc_start: 0.8502 (t60) cc_final: 0.8274 (t60) REVERT: A 1636 MET cc_start: 0.7795 (tpp) cc_final: 0.7452 (tpp) REVERT: A 1637 LYS cc_start: 0.7908 (pttm) cc_final: 0.7404 (ttmt) REVERT: A 1669 TYR cc_start: 0.6537 (m-80) cc_final: 0.6233 (m-10) REVERT: B 150 HIS cc_start: 0.7411 (t70) cc_final: 0.7127 (t70) REVERT: C 137 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8176 (mtp85) REVERT: C 182 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7231 (mtm-85) REVERT: E 134 ARG cc_start: 0.8323 (mtm180) cc_final: 0.8092 (mtm180) outliers start: 34 outliers final: 27 residues processed: 307 average time/residue: 0.1074 time to fit residues: 49.8786 Evaluate side-chains 312 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL 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 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU 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 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 1043 ILE Chi-restraints excluded: chain A residue 1044 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 1524 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 142 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3571 r_free = 0.3571 target = 0.135857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112941 restraints weight = 23093.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116411 restraints weight = 12082.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118700 restraints weight = 7670.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120242 restraints weight = 5609.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121201 restraints weight = 4491.474| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 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 = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15898 Z= 0.121 Angle : 0.533 12.639 21537 Z= 0.276 Chirality : 0.039 0.279 2492 Planarity : 0.003 0.052 2652 Dihedral : 7.714 73.980 2253 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.85 % Allowed : 20.47 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1863 helix: 2.14 (0.16), residues: 1081 sheet: -0.38 (0.57), residues: 80 loop : -0.85 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 511 TYR 0.038 0.001 TYR A 34 PHE 0.013 0.001 PHE A 629 TRP 0.016 0.001 TRP A1610 HIS 0.005 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15898) covalent geometry : angle 0.53327 / 0.28 (21537) hydrogen bonds : bond 0.03396 / 2.21 ( 844) hydrogen bonds : angle 4.12894 / 3.05 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.23 seconds wall clock time: 44 minutes 41.08 seconds (2681.08 seconds total)