Starting phenix.real_space_refine on Fri Jul 3 20:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfu_71614/07_2026/9pfu_71614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfu_71614/07_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_71614/07_2026/9pfu_71614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfu_71614/07_2026/9pfu_71614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfu_71614/07_2026/9pfu_71614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfu_71614/07_2026/9pfu_71614.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 83 5.16 5 C 9934 2.51 5 N 2635 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.66, per 1000 atoms: 0.17 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: 1.12 Conformation dependent library (CDL) restraints added in 589.7 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: 0.32 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: 3.06 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3058 1.33 - 1.45: 3729 1.45 - 1.57: 8948 1.57 - 1.70: 24 1.70 - 1.82: 139 Bond restraints: 15898 Sorted by residual: bond pdb=" N ASP E 164 " pdb=" CA ASP E 164 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" C SER A 870 " pdb=" N LYS A 871 " ideal model delta sigma weight residual 1.332 1.297 0.036 1.38e-02 5.25e+03 6.64e+00 bond pdb=" C LYS A 871 " pdb=" O LYS A 871 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.66e-02 3.63e+03 3.09e+00 bond pdb=" CA ASP E 190 " pdb=" CB ASP E 190 " ideal model delta sigma weight residual 1.527 1.570 -0.042 2.48e-02 1.63e+03 2.91e+00 bond pdb=" N ASN A 538 " pdb=" CA ASN A 538 " ideal model delta sigma weight residual 1.455 1.478 -0.022 1.32e-02 5.74e+03 2.84e+00 ... (remaining 15893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 21373 2.91 - 5.82: 141 5.82 - 8.73: 16 8.73 - 11.64: 6 11.64 - 14.55: 1 Bond angle restraints: 21537 Sorted by residual: angle pdb=" N LYS A 871 " pdb=" CA LYS A 871 " pdb=" CB LYS A 871 " ideal model delta sigma weight residual 112.63 104.60 8.03 1.61e+00 3.86e-01 2.49e+01 angle pdb=" CB MET A1396 " pdb=" CG MET A1396 " pdb=" SD MET A1396 " ideal model delta sigma weight residual 112.70 98.15 14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CB MET E 195 " pdb=" CG MET E 195 " pdb=" SD MET E 195 " ideal model delta sigma weight residual 112.70 123.68 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA LEU B 146 " pdb=" CB LEU B 146 " pdb=" CG LEU B 146 " ideal model delta sigma weight residual 116.30 127.74 -11.44 3.50e+00 8.16e-02 1.07e+01 ... (remaining 21532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8548 17.90 - 35.80: 915 35.80 - 53.70: 170 53.70 - 71.61: 31 71.61 - 89.51: 18 Dihedral angle restraints: 9682 sinusoidal: 4111 harmonic: 5571 Sorted by residual: dihedral pdb=" CA GLU A1584 " pdb=" C GLU A1584 " pdb=" N GLN A1585 " pdb=" CA GLN A1585 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ILE A1529 " pdb=" C ILE A1529 " pdb=" N ASN A1530 " pdb=" CA ASN A1530 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP A 865 " pdb=" C ASP A 865 " pdb=" N MET A 866 " pdb=" CA MET A 866 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2022 0.054 - 0.108: 418 0.108 - 0.162: 42 0.162 - 0.216: 8 0.216 - 0.270: 2 Chirality restraints: 2492 Sorted by residual: chirality pdb=" CA MET A 360 " pdb=" N MET A 360 " pdb=" C MET A 360 " pdb=" CB MET A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2489 not shown) Planarity restraints: 2652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 190 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" CG ASP E 190 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP E 190 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP E 190 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 682 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C ASN A 682 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 682 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 683 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1132 " -0.017 2.00e-02 2.50e+03 1.44e-02 4.13e+00 pdb=" CG TYR A1132 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A1132 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A1132 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A1132 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A1132 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1132 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1132 " 0.001 2.00e-02 2.50e+03 ... (remaining 2649 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2661 2.77 - 3.30: 15412 3.30 - 3.83: 26383 3.83 - 4.37: 30068 4.37 - 4.90: 52539 Nonbonded interactions: 127063 Sorted by model distance: nonbonded pdb=" O THR A1259 " pdb=" OG1 THR A1359 " model vdw 2.236 3.040 nonbonded pdb=" ND2 ASN A1304 " pdb=" O VAL A1431 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASN A 603 " pdb=" NZ LYS B 180 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A1376 " pdb=" O ILE A1419 " model vdw 2.260 3.040 nonbonded pdb=" O ALA A1052 " pdb=" OG1 THR A1056 " model vdw 2.263 3.040 ... (remaining 127058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 183) selection = (chain 'C' and resid 130 through 183) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- 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= 0.139 Angle : 0.657 14.547 21537 Z= 0.341 Chirality : 0.043 0.270 2492 Planarity : 0.004 0.048 2652 Dihedral : 15.156 89.507 6068 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1863 helix: 1.72 (0.15), residues: 1078 sheet: -1.08 (0.59), residues: 77 loop : -1.04 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.035 0.001 TYR A1132 PHE 0.024 0.001 PHE A1668 TRP 0.023 0.001 TRP A1610 HIS 0.004 0.001 HIS A1487 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (15898) covalent geometry : angle 0.65678 / 0.34 (21537) hydrogen bonds : bond 0.11766 / 7.38 ( 844) hydrogen bonds : angle 5.48814 / 4.01 ( 2463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.401 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: 0.1139 time to fit residues: 62.5957 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 : 0.405 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.143461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120741 restraints weight = 23167.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124325 restraints weight = 12100.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126736 restraints weight = 7696.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128295 restraints weight = 5578.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129432 restraints weight = 4453.180| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 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 = 0.3491 r_free = 0.3491 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: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15898 Z= 0.144 Angle : 0.546 12.029 21537 Z= 0.286 Chirality : 0.040 0.201 2492 Planarity : 0.004 0.048 2652 Dihedral : 7.841 73.946 2253 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 10.70 % Favored : 87.97 % 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: 1.18 (0.19), residues: 1863 helix: 1.94 (0.15), residues: 1093 sheet: -0.92 (0.57), residues: 80 loop : -0.91 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1409 TYR 0.018 0.001 TYR A 917 PHE 0.024 0.001 PHE A 629 TRP 0.013 0.001 TRP A 785 HIS 0.004 0.001 HIS A 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15898) covalent geometry : angle 0.54574 / 0.29 (21537) hydrogen bonds : bond 0.03643 / 2.35 ( 844) hydrogen bonds : angle 4.59311 / 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 339 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 316 time to evaluate : 0.618 Fit side-chains REVERT: A 59 MET cc_start: 0.8212 (mtm) cc_final: 0.7853 (mtm) REVERT: A 354 LYS cc_start: 0.7520 (mmtp) cc_final: 0.6770 (pttp) REVERT: A 473 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7756 (t80) REVERT: A 539 ASP cc_start: 0.8178 (t0) cc_final: 0.7895 (t0) REVERT: A 774 MET cc_start: 0.6882 (mmm) cc_final: 0.6630 (mmt) REVERT: A 851 ILE cc_start: 0.8034 (tp) cc_final: 0.7731 (tp) REVERT: A 865 ASP cc_start: 0.7879 (p0) cc_final: 0.7582 (p0) REVERT: A 1135 GLU cc_start: 0.8700 (tp30) cc_final: 0.8068 (tp30) REVERT: A 1141 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 1339 ARG cc_start: 0.7268 (mmt-90) cc_final: 0.7031 (mmt-90) REVERT: A 1536 ASN cc_start: 0.7213 (m-40) cc_final: 0.6950 (m-40) REVERT: C 182 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8053 (mpt-90) outliers start: 23 outliers final: 12 residues processed: 326 average time/residue: 0.1132 time to fit residues: 55.5652 Evaluate side-chains 305 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 291 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 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 A residue 1623 CYS 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: 6.9990 chunk 74 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN A 689 ASN A 705 ASN A 876 ASN A1335 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115392 restraints weight = 23369.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118886 restraints weight = 12248.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121226 restraints weight = 7797.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122787 restraints weight = 5678.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123839 restraints weight = 4538.918| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15898 Z= 0.169 Angle : 0.533 7.886 21537 Z= 0.280 Chirality : 0.040 0.212 2492 Planarity : 0.003 0.041 2652 Dihedral : 7.818 73.901 2253 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.56 % Allowed : 13.94 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1863 helix: 2.02 (0.15), residues: 1091 sheet: -1.05 (0.55), residues: 85 loop : -0.92 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1409 TYR 0.023 0.002 TYR A 125 PHE 0.018 0.001 PHE A 424 TRP 0.014 0.001 TRP A 785 HIS 0.004 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (15898) covalent geometry : angle 0.53285 / 0.28 (21537) hydrogen bonds : bond 0.03716 / 2.41 ( 844) hydrogen bonds : angle 4.40514 / 3.24 ( 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 325 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.605 Fit side-chains REVERT: A 59 MET cc_start: 0.8315 (mtm) cc_final: 0.7968 (mtm) REVERT: A 354 LYS cc_start: 0.7594 (mmtp) cc_final: 0.6847 (pttp) REVERT: A 360 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7259 (mtp) REVERT: A 473 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 511 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6997 (mtp85) REVERT: A 774 MET cc_start: 0.7415 (mmm) cc_final: 0.7189 (mmt) REVERT: A 834 TYR cc_start: 0.7948 (m-80) cc_final: 0.7622 (m-80) REVERT: A 851 ILE cc_start: 0.8144 (tp) cc_final: 0.7789 (tp) REVERT: A 865 ASP cc_start: 0.8017 (p0) cc_final: 0.7752 (p0) REVERT: A 1135 GLU cc_start: 0.8737 (tp30) cc_final: 0.7955 (tp30) REVERT: A 1141 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 1536 ASN cc_start: 0.7278 (m-40) cc_final: 0.7009 (m-40) REVERT: A 1669 TYR cc_start: 0.6885 (m-80) cc_final: 0.6533 (m-10) REVERT: E 187 MET cc_start: 0.7766 (ptm) cc_final: 0.7289 (ptp) outliers start: 27 outliers final: 15 residues processed: 309 average time/residue: 0.1101 time to fit residues: 51.6364 Evaluate side-chains 303 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 103 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 185 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN A 689 ASN A1387 ASN ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115040 restraints weight = 23313.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118544 restraints weight = 12238.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120926 restraints weight = 7809.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122416 restraints weight = 5688.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123492 restraints weight = 4588.072| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1775 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= 0.130 Angle : 0.494 8.546 21537 Z= 0.262 Chirality : 0.039 0.228 2492 Planarity : 0.003 0.038 2652 Dihedral : 7.777 73.958 2253 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.79 % Allowed : 14.69 % Favored : 83.52 % 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: 2.06 (0.16), residues: 1096 sheet: -0.86 (0.57), residues: 85 loop : -0.89 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 182 TYR 0.013 0.001 TYR A 34 PHE 0.017 0.001 PHE A 629 TRP 0.011 0.001 TRP A1610 HIS 0.003 0.001 HIS A1022 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15898) covalent geometry : angle 0.49433 / 0.26 (21537) hydrogen bonds : bond 0.03503 / 2.29 ( 844) hydrogen bonds : angle 4.27478 / 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 336 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8409 (mtm) cc_final: 0.8094 (mtm) REVERT: A 87 PHE cc_start: 0.7957 (m-80) cc_final: 0.7670 (m-80) REVERT: A 354 LYS cc_start: 0.7653 (mmtp) cc_final: 0.6946 (pttp) REVERT: A 360 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7080 (tpp) REVERT: A 473 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7896 (t80) REVERT: A 851 ILE cc_start: 0.8200 (tp) cc_final: 0.7819 (tp) REVERT: A 865 ASP cc_start: 0.7943 (p0) cc_final: 0.7719 (p0) REVERT: A 1141 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8257 (mp) REVERT: A 1536 ASN cc_start: 0.7282 (m-40) cc_final: 0.7007 (m-40) REVERT: A 1574 TYR cc_start: 0.8558 (t80) cc_final: 0.8189 (t80) REVERT: A 1586 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8307 (ptpp) REVERT: A 1669 TYR cc_start: 0.6699 (m-80) cc_final: 0.6234 (m-10) REVERT: E 187 MET cc_start: 0.7751 (ptm) cc_final: 0.7264 (ptp) REVERT: E 190 ASP cc_start: 0.8217 (p0) cc_final: 0.7833 (p0) outliers start: 31 outliers final: 20 residues processed: 320 average time/residue: 0.1110 time to fit residues: 52.7759 Evaluate side-chains 310 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 625 VAL Chi-restraints excluded: chain A residue 674 LYS 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 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 B residue 164 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 39 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN A 632 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114333 restraints weight = 23272.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117824 restraints weight = 12169.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120170 restraints weight = 7748.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121718 restraints weight = 5639.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122768 restraints weight = 4519.111| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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= 0.129 Angle : 0.492 7.659 21537 Z= 0.260 Chirality : 0.039 0.253 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.745 73.930 2253 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.26 % Allowed : 16.14 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1863 helix: 2.14 (0.16), residues: 1087 sheet: -0.80 (0.56), residues: 85 loop : -0.89 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 182 TYR 0.029 0.001 TYR A 34 PHE 0.015 0.001 PHE A 629 TRP 0.014 0.001 TRP A 780 HIS 0.003 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15898) covalent geometry : angle 0.49156 / 0.26 (21537) hydrogen bonds : bond 0.03461 / 2.26 ( 844) hydrogen bonds : angle 4.20392 / 3.10 ( 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 335 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8362 (mtm) cc_final: 0.8057 (mtm) REVERT: A 87 PHE cc_start: 0.7964 (m-80) cc_final: 0.7729 (m-80) REVERT: A 354 LYS cc_start: 0.7685 (mmtp) cc_final: 0.6974 (pttp) REVERT: A 360 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7233 (tpp) REVERT: A 473 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7909 (t80) REVERT: A 677 ILE cc_start: 0.8994 (tt) cc_final: 0.8762 (tt) REVERT: A 684 TYR cc_start: 0.8063 (p90) cc_final: 0.7827 (p90) REVERT: A 851 ILE cc_start: 0.8334 (tp) cc_final: 0.7924 (tp) REVERT: A 906 GLU cc_start: 0.7550 (tt0) cc_final: 0.7133 (tp30) REVERT: A 1136 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8453 (mttm) REVERT: A 1141 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 1409 ARG cc_start: 0.7470 (ttm110) cc_final: 0.7197 (ttm110) REVERT: A 1536 ASN cc_start: 0.7292 (m-40) cc_final: 0.7011 (m-40) REVERT: A 1586 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8463 (ptpp) REVERT: A 1637 LYS cc_start: 0.7911 (pttm) cc_final: 0.7428 (ttmt) REVERT: A 1669 TYR cc_start: 0.6685 (m-80) cc_final: 0.6141 (m-10) REVERT: C 137 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8406 (mmm-85) REVERT: C 182 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7276 (mtm-85) REVERT: E 187 MET cc_start: 0.7808 (ptm) cc_final: 0.7482 (ptt) REVERT: E 190 ASP cc_start: 0.8126 (p0) cc_final: 0.7722 (p0) outliers start: 39 outliers final: 25 residues processed: 317 average time/residue: 0.1049 time to fit residues: 50.5428 Evaluate side-chains 311 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 705 ASN Chi-restraints excluded: chain A residue 741 THR 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 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 1524 THR 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 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: 2.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 46 optimal weight: 7.9990 chunk 143 optimal weight: 0.0050 overall best weight: 1.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 638 GLN 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 = 0.3594 r_free = 0.3594 target = 0.137980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114743 restraints weight = 23202.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118239 restraints weight = 12278.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120613 restraints weight = 7905.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122197 restraints weight = 5774.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123240 restraints weight = 4629.577| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15898 Z= 0.114 Angle : 0.495 8.304 21537 Z= 0.259 Chirality : 0.038 0.258 2492 Planarity : 0.003 0.047 2652 Dihedral : 7.719 73.932 2253 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.20 % Allowed : 17.87 % Favored : 79.93 % 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: 2.13 (0.16), residues: 1097 sheet: -0.62 (0.58), residues: 80 loop : -0.90 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 182 TYR 0.020 0.001 TYR A1376 PHE 0.013 0.001 PHE A1668 TRP 0.028 0.002 TRP A 780 HIS 0.002 0.000 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15898) covalent geometry : angle 0.49463 / 0.26 (21537) hydrogen bonds : bond 0.03355 / 2.18 ( 844) hydrogen bonds : angle 4.16291 / 3.07 ( 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 333 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8355 (mtm) cc_final: 0.7958 (mtm) REVERT: A 87 PHE cc_start: 0.7928 (m-80) cc_final: 0.7664 (m-80) REVERT: A 354 LYS cc_start: 0.7689 (mmtp) cc_final: 0.6976 (pttp) REVERT: A 360 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7124 (tpp) REVERT: A 473 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7928 (t80) REVERT: A 677 ILE cc_start: 0.8967 (tt) cc_final: 0.8725 (tt) REVERT: A 684 TYR cc_start: 0.8064 (p90) cc_final: 0.7831 (p90) REVERT: A 851 ILE cc_start: 0.8245 (tp) cc_final: 0.7845 (tp) REVERT: A 906 GLU cc_start: 0.7512 (tt0) cc_final: 0.7145 (tp30) REVERT: A 1141 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 1409 ARG cc_start: 0.7450 (ttm110) cc_final: 0.7167 (ttm110) REVERT: A 1574 TYR cc_start: 0.8558 (t80) cc_final: 0.8123 (t80) REVERT: A 1586 LYS cc_start: 0.8722 (ptpt) cc_final: 0.8368 (ptpp) REVERT: A 1637 LYS cc_start: 0.7901 (pttm) cc_final: 0.7394 (ttmt) REVERT: A 1669 TYR cc_start: 0.6718 (m-80) cc_final: 0.6236 (m-10) REVERT: C 137 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.8450 (mmm-85) REVERT: C 182 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7233 (mtm-85) REVERT: E 187 MET cc_start: 0.7759 (ptm) cc_final: 0.7438 (ptt) REVERT: E 190 ASP cc_start: 0.8123 (p0) cc_final: 0.7776 (p0) outliers start: 38 outliers final: 27 residues processed: 320 average time/residue: 0.1166 time to fit residues: 56.1354 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 : 0.433 ------------------------------------------------------------------------------- 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 447 CYS Chi-restraints excluded: chain A residue 459 SER 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 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 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 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 140 GLU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 ** A1526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 HIS ** A1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113835 restraints weight = 23098.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117335 restraints weight = 12189.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119660 restraints weight = 7788.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121214 restraints weight = 5702.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122169 restraints weight = 4582.012| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15898 Z= 0.125 Angle : 0.501 8.085 21537 Z= 0.262 Chirality : 0.039 0.259 2492 Planarity : 0.003 0.054 2652 Dihedral : 7.700 73.898 2253 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.08 % Allowed : 18.51 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1863 helix: 2.18 (0.16), residues: 1091 sheet: -0.57 (0.58), residues: 80 loop : -0.83 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 182 TYR 0.016 0.001 TYR A1522 PHE 0.013 0.001 PHE A 424 TRP 0.016 0.001 TRP A1610 HIS 0.011 0.001 HIS A1685 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (15898) covalent geometry : angle 0.50083 / 0.26 (21537) hydrogen bonds : bond 0.03408 / 2.23 ( 844) hydrogen bonds : angle 4.12984 / 3.05 ( 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 338 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8369 (mtm) cc_final: 0.7917 (mtm) REVERT: A 87 PHE cc_start: 0.7930 (m-80) cc_final: 0.7692 (m-80) REVERT: A 354 LYS cc_start: 0.7672 (mmtp) cc_final: 0.6940 (pttp) REVERT: A 360 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7305 (tpp) REVERT: A 473 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7959 (t80) REVERT: A 499 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7108 (pp) REVERT: A 677 ILE cc_start: 0.8942 (tt) cc_final: 0.8705 (tt) REVERT: A 684 TYR cc_start: 0.8099 (p90) cc_final: 0.7852 (p90) REVERT: A 851 ILE cc_start: 0.8214 (tp) cc_final: 0.7794 (tp) REVERT: A 906 GLU cc_start: 0.7601 (tt0) cc_final: 0.7215 (tp30) REVERT: A 1141 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 1409 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7168 (ttm110) REVERT: A 1522 TYR cc_start: 0.8122 (m-10) cc_final: 0.7909 (m-10) REVERT: A 1536 ASN cc_start: 0.6903 (m-40) cc_final: 0.6691 (m-40) REVERT: A 1574 TYR cc_start: 0.8531 (t80) cc_final: 0.8085 (t80) REVERT: A 1584 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 1586 LYS cc_start: 0.8767 (ptpt) cc_final: 0.8359 (ptpp) REVERT: A 1637 LYS cc_start: 0.7877 (pttm) cc_final: 0.7357 (ttmt) REVERT: A 1669 TYR cc_start: 0.6618 (m-80) cc_final: 0.6206 (m-10) REVERT: C 137 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: C 182 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7230 (mtm-85) REVERT: E 187 MET cc_start: 0.7812 (ptm) cc_final: 0.7540 (ptt) REVERT: E 190 ASP cc_start: 0.8102 (p0) cc_final: 0.7819 (p0) outliers start: 36 outliers final: 25 residues processed: 323 average time/residue: 0.1034 time to fit residues: 50.7056 Evaluate side-chains 317 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 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 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 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 148 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1098 GLN ** A1526 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114417 restraints weight = 23172.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117917 restraints weight = 12147.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120248 restraints weight = 7740.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121830 restraints weight = 5652.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122732 restraints weight = 4525.331| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2226 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= 0.117 Angle : 0.502 9.086 21537 Z= 0.263 Chirality : 0.039 0.272 2492 Planarity : 0.003 0.052 2652 Dihedral : 7.689 73.896 2253 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.85 % Allowed : 19.38 % Favored : 78.77 % 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: 1.49 (0.20), residues: 1863 helix: 2.17 (0.16), residues: 1091 sheet: -0.45 (0.58), residues: 80 loop : -0.78 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 182 TYR 0.031 0.001 TYR A 34 PHE 0.013 0.001 PHE A 629 TRP 0.015 0.001 TRP A1610 HIS 0.005 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15898) covalent geometry : angle 0.50204 / 0.26 (21537) hydrogen bonds : bond 0.03358 / 2.19 ( 844) hydrogen bonds : angle 4.11160 / 3.04 ( 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 321 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 289 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8321 (mtm) cc_final: 0.7921 (mtm) REVERT: A 87 PHE cc_start: 0.7884 (m-80) cc_final: 0.7647 (m-80) REVERT: A 354 LYS cc_start: 0.7702 (mmtp) cc_final: 0.6970 (pttp) REVERT: A 360 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7243 (tpp) REVERT: A 473 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8016 (t80) REVERT: A 499 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7107 (pp) REVERT: A 677 ILE cc_start: 0.8946 (tt) cc_final: 0.8707 (tt) REVERT: A 684 TYR cc_start: 0.8102 (p90) cc_final: 0.7871 (p90) REVERT: A 851 ILE cc_start: 0.8230 (tp) cc_final: 0.7807 (tp) REVERT: A 906 GLU cc_start: 0.7611 (tt0) cc_final: 0.7248 (tp30) REVERT: A 1136 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8434 (mttm) REVERT: A 1141 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 1158 ASP cc_start: 0.7759 (p0) cc_final: 0.7545 (p0) REVERT: A 1409 ARG cc_start: 0.7473 (ttm110) cc_final: 0.7172 (ttm110) REVERT: A 1536 ASN cc_start: 0.6861 (m-40) cc_final: 0.6612 (m-40) REVERT: A 1574 TYR cc_start: 0.8529 (t80) cc_final: 0.8059 (t80) REVERT: A 1586 LYS cc_start: 0.8765 (ptpt) cc_final: 0.8368 (ptpp) REVERT: A 1637 LYS cc_start: 0.7888 (pttm) cc_final: 0.7384 (ttmt) REVERT: A 1669 TYR cc_start: 0.6549 (m-80) cc_final: 0.6172 (m-10) REVERT: A 1685 HIS cc_start: 0.7749 (m-70) cc_final: 0.7438 (m-70) REVERT: C 137 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8251 (mmm-85) REVERT: C 182 ARG cc_start: 0.7702 (tpp80) cc_final: 0.7226 (mtm-85) REVERT: E 187 MET cc_start: 0.7807 (ptm) cc_final: 0.7525 (ptt) REVERT: E 190 ASP cc_start: 0.8101 (p0) cc_final: 0.7839 (p0) outliers start: 32 outliers final: 24 residues processed: 308 average time/residue: 0.1050 time to fit residues: 49.0540 Evaluate side-chains 313 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU 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 705 ASN 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 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 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: 7.9990 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 155 optimal weight: 0.0470 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114546 restraints weight = 23037.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118053 restraints weight = 12126.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120395 restraints weight = 7725.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121962 restraints weight = 5630.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122983 restraints weight = 4504.868| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2246 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= 0.113 Angle : 0.507 9.104 21537 Z= 0.265 Chirality : 0.039 0.446 2492 Planarity : 0.003 0.051 2652 Dihedral : 7.676 73.892 2253 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.85 % Allowed : 19.43 % Favored : 78.72 % 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: 1.51 (0.20), residues: 1863 helix: 2.18 (0.16), residues: 1087 sheet: -0.40 (0.58), residues: 80 loop : -0.76 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 182 TYR 0.026 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 0.00260 / 0.11 (15898) covalent geometry : angle 0.50671 / 0.27 (21537) hydrogen bonds : bond 0.03320 / 2.16 ( 844) hydrogen bonds : angle 4.09829 / 3.03 ( 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 324 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8351 (mtm) cc_final: 0.7952 (mtm) REVERT: A 87 PHE cc_start: 0.7860 (m-80) cc_final: 0.7632 (m-80) REVERT: A 354 LYS cc_start: 0.7709 (mmtp) cc_final: 0.6997 (pttp) REVERT: A 360 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7193 (tpp) REVERT: A 473 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8011 (t80) REVERT: A 499 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7104 (pp) REVERT: A 677 ILE cc_start: 0.8950 (tt) cc_final: 0.8712 (tt) REVERT: A 684 TYR cc_start: 0.8115 (p90) cc_final: 0.7882 (p90) REVERT: A 774 MET cc_start: 0.7012 (mmm) cc_final: 0.6595 (mmt) REVERT: A 851 ILE cc_start: 0.8205 (tp) cc_final: 0.7787 (tp) REVERT: A 866 MET cc_start: 0.8479 (ptm) cc_final: 0.8213 (ptp) REVERT: A 906 GLU cc_start: 0.7656 (tt0) cc_final: 0.7254 (tp30) REVERT: A 1136 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8473 (mttm) REVERT: A 1141 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 1409 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7130 (ttm110) REVERT: A 1536 ASN cc_start: 0.6826 (m-40) cc_final: 0.6591 (m-40) REVERT: A 1574 TYR cc_start: 0.8515 (t80) cc_final: 0.8038 (t80) REVERT: A 1584 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 1586 LYS cc_start: 0.8778 (ptpt) cc_final: 0.8387 (ptpp) REVERT: A 1637 LYS cc_start: 0.7912 (pttm) cc_final: 0.7402 (ttmt) REVERT: A 1669 TYR cc_start: 0.6569 (m-80) cc_final: 0.6179 (m-10) REVERT: A 1685 HIS cc_start: 0.7724 (m-70) cc_final: 0.7443 (m-70) REVERT: C 137 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8277 (mmm-85) REVERT: C 182 ARG cc_start: 0.7689 (tpp80) cc_final: 0.7211 (mtm-85) REVERT: E 187 MET cc_start: 0.7804 (ptm) cc_final: 0.7557 (ptt) REVERT: E 190 ASP cc_start: 0.8072 (p0) cc_final: 0.7847 (p0) outliers start: 32 outliers final: 26 residues processed: 313 average time/residue: 0.1039 time to fit residues: 48.8135 Evaluate side-chains 313 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 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 705 ASN 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 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 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: 0.9990 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.137264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114272 restraints weight = 23117.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117724 restraints weight = 12098.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120045 restraints weight = 7723.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121593 restraints weight = 5647.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122487 restraints weight = 4545.260| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2332 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= 0.126 Angle : 0.527 10.716 21537 Z= 0.273 Chirality : 0.040 0.381 2492 Planarity : 0.003 0.051 2652 Dihedral : 7.678 73.878 2253 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.14 % Allowed : 19.49 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1863 helix: 2.15 (0.16), residues: 1087 sheet: -0.39 (0.58), residues: 80 loop : -0.77 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.031 0.001 TYR A 211 PHE 0.013 0.001 PHE A 629 TRP 0.016 0.001 TRP A1610 HIS 0.004 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15898) covalent geometry : angle 0.52729 / 0.27 (21537) hydrogen bonds : bond 0.03365 / 2.19 ( 844) hydrogen bonds : angle 4.10571 / 3.04 ( 2463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.8352 (mtm) cc_final: 0.7962 (mtm) REVERT: A 87 PHE cc_start: 0.7833 (m-80) cc_final: 0.7611 (m-80) REVERT: A 360 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7206 (tpp) REVERT: A 473 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8021 (t80) REVERT: A 499 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7144 (pp) REVERT: A 677 ILE cc_start: 0.8962 (tt) cc_final: 0.8717 (tt) REVERT: A 684 TYR cc_start: 0.8097 (p90) cc_final: 0.7849 (p90) REVERT: A 774 MET cc_start: 0.7193 (mmm) cc_final: 0.6828 (mmt) REVERT: A 851 ILE cc_start: 0.8216 (tp) cc_final: 0.7798 (tp) REVERT: A 866 MET cc_start: 0.8470 (ptm) cc_final: 0.8168 (ptp) REVERT: A 906 GLU cc_start: 0.7672 (tt0) cc_final: 0.7262 (tp30) REVERT: A 989 ASP cc_start: 0.9337 (t0) cc_final: 0.9036 (t70) REVERT: A 1136 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8475 (mttm) REVERT: A 1141 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 1409 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7165 (ttm110) REVERT: A 1536 ASN cc_start: 0.6831 (m-40) cc_final: 0.6602 (m-40) REVERT: A 1574 TYR cc_start: 0.8542 (t80) cc_final: 0.8051 (t80) REVERT: A 1586 LYS cc_start: 0.8781 (ptpt) cc_final: 0.8377 (ptpp) REVERT: A 1637 LYS cc_start: 0.7871 (pttm) cc_final: 0.7407 (ttmt) REVERT: A 1669 TYR cc_start: 0.6577 (m-80) cc_final: 0.6181 (m-10) REVERT: C 137 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8304 (mmm-85) REVERT: C 182 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7218 (mtm-85) REVERT: E 187 MET cc_start: 0.7830 (ptm) cc_final: 0.7606 (ptt) outliers start: 37 outliers final: 27 residues processed: 313 average time/residue: 0.1066 time to fit residues: 50.4997 Evaluate side-chains 316 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 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 705 ASN 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 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 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: 0.9980 chunk 127 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 A 876 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114831 restraints weight = 23142.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118364 restraints weight = 12208.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120694 restraints weight = 7778.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122169 restraints weight = 5685.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123276 restraints weight = 4596.311| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2331 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= 0.115 Angle : 0.522 11.983 21537 Z= 0.271 Chirality : 0.039 0.346 2492 Planarity : 0.003 0.051 2652 Dihedral : 7.673 73.888 2253 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.02 % Allowed : 19.78 % 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: 1.47 (0.20), residues: 1863 helix: 2.14 (0.16), residues: 1086 sheet: -0.37 (0.58), residues: 80 loop : -0.76 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 134 TYR 0.027 0.001 TYR A 211 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 0.00265 / 0.12 (15898) covalent geometry : angle 0.52175 / 0.27 (21537) hydrogen bonds : bond 0.03307 / 2.15 ( 844) hydrogen bonds : angle 4.09306 / 3.02 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2274.79 seconds wall clock time: 40 minutes 14.14 seconds (2414.14 seconds total)