Starting phenix.real_space_refine on Wed Mar 4 13:37:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wy1_66359/03_2026/9wy1_66359_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wy1_66359/03_2026/9wy1_66359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wy1_66359/03_2026/9wy1_66359_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wy1_66359/03_2026/9wy1_66359_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wy1_66359/03_2026/9wy1_66359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wy1_66359/03_2026/9wy1_66359.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 1 5.49 5 S 78 5.16 5 C 8601 2.51 5 N 2090 2.21 5 O 2228 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12998 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1521, 12403 Classifications: {'peptide': 1521} Link IDs: {'PTRANS': 67, 'TRANS': 1453} Chain breaks: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 567 Unusual residues: {'AV0': 2, 'ERG': 13, 'POV': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 12998 At special positions: 0 Unit cell: (108.04, 121.36, 122.84, 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 78 16.00 P 1 15.00 O 2228 8.00 N 2090 7.00 C 8601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.06 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 Simple disulfide: pdb=" SG CYS A1620 " - pdb=" SG CYS A1625 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A1849 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 446.9 milliseconds 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 64.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 197 removed outlier: 4.042A pdb=" N ARG A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.531A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 4.003A pdb=" N LYS A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 321 through 337 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.686A pdb=" N LYS A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 406 " --> pdb=" O ILE A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 406' Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.516A pdb=" N LEU A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.619A pdb=" N ARG A 422 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 452 through 468 removed outlier: 4.283A pdb=" N ILE A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 518 removed outlier: 3.967A pdb=" N LEU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 553 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 560 through 581 removed outlier: 3.924A pdb=" N VAL A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 615 through 630 Processing helix chain 'A' and resid 631 through 640 removed outlier: 3.889A pdb=" N TYR A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.515A pdb=" N ARG A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 711 removed outlier: 3.896A pdb=" N ILE A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.832A pdb=" N ILE A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.666A pdb=" N ARG A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 734 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 764 Processing helix chain 'A' and resid 768 through 774 removed outlier: 3.611A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 813 through 826 Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 880 through 899 Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 958 through 972 removed outlier: 3.782A pdb=" N ARG A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 3.699A pdb=" N VAL A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 3.560A pdb=" N HIS A1088 " --> pdb=" O ASP A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1093 Processing helix chain 'A' and resid 1108 through 1113 Processing helix chain 'A' and resid 1114 through 1119 Processing helix chain 'A' and resid 1120 through 1123 Processing helix chain 'A' and resid 1172 through 1187 removed outlier: 4.805A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A1180 " --> pdb=" O PHE A1176 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG A1182 " --> pdb=" O THR A1178 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 removed outlier: 3.544A pdb=" N THR A1206 " --> pdb=" O THR A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1233 Processing helix chain 'A' and resid 1267 through 1271 removed outlier: 3.976A pdb=" N MET A1270 " --> pdb=" O GLY A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1280 removed outlier: 3.752A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 4.007A pdb=" N THR A1289 " --> pdb=" O ASP A1285 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS A1294 " --> pdb=" O PHE A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1324 removed outlier: 3.781A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A1301 " --> pdb=" O PHE A1297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A1302 " --> pdb=" O HIS A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1353 removed outlier: 3.605A pdb=" N VAL A1352 " --> pdb=" O PHE A1348 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A1353 " --> pdb=" O GLN A1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1348 through 1353' Processing helix chain 'A' and resid 1353 through 1368 Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 3.856A pdb=" N GLU A1377 " --> pdb=" O ILE A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1397 removed outlier: 3.583A pdb=" N THR A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1444 removed outlier: 3.616A pdb=" N SER A1443 " --> pdb=" O SER A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1467 Processing helix chain 'A' and resid 1473 through 1485 Processing helix chain 'A' and resid 1495 through 1511 Processing helix chain 'A' and resid 1521 through 1532 Processing helix chain 'A' and resid 1559 through 1565 removed outlier: 3.634A pdb=" N ILE A1565 " --> pdb=" O ILE A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1583 Processing helix chain 'A' and resid 1598 through 1623 Proline residue: A1609 - end of helix removed outlier: 3.769A pdb=" N ASN A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A1621 " --> pdb=" O LEU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1626 No H-bonds generated for 'chain 'A' and resid 1624 through 1626' Processing helix chain 'A' and resid 1627 through 1635 Processing helix chain 'A' and resid 1638 through 1665 removed outlier: 3.727A pdb=" N ALA A1643 " --> pdb=" O GLY A1639 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A1648 " --> pdb=" O GLY A1644 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A1649 " --> pdb=" O ILE A1645 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A1665 " --> pdb=" O MET A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1695 removed outlier: 3.737A pdb=" N ILE A1674 " --> pdb=" O VAL A1670 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1753 Processing helix chain 'A' and resid 1754 through 1759 Processing helix chain 'A' and resid 1762 through 1775 removed outlier: 3.577A pdb=" N PHE A1766 " --> pdb=" O LYS A1762 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1817 removed outlier: 3.531A pdb=" N LYS A1798 " --> pdb=" O LYS A1794 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A1800 " --> pdb=" O MET A1796 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1802 " --> pdb=" O LYS A1798 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A1815 " --> pdb=" O PHE A1811 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1824 Processing helix chain 'A' and resid 1828 through 1832 removed outlier: 3.605A pdb=" N ASP A1831 " --> pdb=" O HIS A1828 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A1832 " --> pdb=" O ILE A1829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1828 through 1832' Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 781 removed outlier: 3.579A pdb=" N HIS A 778 " --> pdb=" O ARG A 791 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 780 " --> pdb=" O THR A 789 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1071 removed outlier: 3.853A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 843 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 13.157A pdb=" N VAL A1148 " --> pdb=" O HIS A1238 " (cutoff:3.500A) removed outlier: 16.208A pdb=" N GLU A1240 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 16.935A pdb=" N ILE A1150 " --> pdb=" O GLU A1240 " (cutoff:3.500A) removed outlier: 13.253A pdb=" N TYR A1242 " --> pdb=" O ILE A1150 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLY A1152 " --> pdb=" O TYR A1242 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N CYS A1244 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A1154 " --> pdb=" O CYS A1244 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LYS A1246 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR A1156 " --> pdb=" O LYS A1246 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2271 1.33 - 1.45: 3522 1.45 - 1.57: 7446 1.57 - 1.69: 12 1.69 - 1.81: 124 Bond restraints: 13375 Sorted by residual: bond pdb=" C ILE A1829 " pdb=" O ILE A1829 " ideal model delta sigma weight residual 1.237 1.283 -0.046 1.29e-02 6.01e+03 1.27e+01 bond pdb=" N ILE A1829 " pdb=" CA ILE A1829 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C LEU A 446 " pdb=" O LEU A 446 " ideal model delta sigma weight residual 1.237 1.275 -0.038 1.17e-02 7.31e+03 1.06e+01 bond pdb=" N ILE A1780 " pdb=" CA ILE A1780 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL A1526 " pdb=" CA VAL A1526 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.64e+00 ... (remaining 13370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17379 2.01 - 4.01: 758 4.01 - 6.02: 67 6.02 - 8.02: 5 8.02 - 10.03: 3 Bond angle restraints: 18212 Sorted by residual: angle pdb=" C GLY A1830 " pdb=" N ASP A1831 " pdb=" CA ASP A1831 " ideal model delta sigma weight residual 121.19 130.43 -9.24 1.59e+00 3.96e-01 3.37e+01 angle pdb=" C HIS A1828 " pdb=" CA HIS A1828 " pdb=" CB HIS A1828 " ideal model delta sigma weight residual 109.62 119.65 -10.03 1.79e+00 3.12e-01 3.14e+01 angle pdb=" O GLY A1830 " pdb=" C GLY A1830 " pdb=" N ASP A1831 " ideal model delta sigma weight residual 122.73 128.50 -5.77 1.12e+00 7.97e-01 2.65e+01 angle pdb=" N ASP A1850 " pdb=" CA ASP A1850 " pdb=" C ASP A1850 " ideal model delta sigma weight residual 114.09 106.99 7.10 1.55e+00 4.16e-01 2.10e+01 angle pdb=" C ARG A1781 " pdb=" N PRO A1782 " pdb=" CA PRO A1782 " ideal model delta sigma weight residual 119.66 122.92 -3.26 7.20e-01 1.93e+00 2.05e+01 ... (remaining 18207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 8347 35.13 - 70.26: 306 70.26 - 105.39: 38 105.39 - 140.51: 18 140.51 - 175.64: 3 Dihedral angle restraints: 8712 sinusoidal: 4247 harmonic: 4465 Sorted by residual: dihedral pdb=" C HIS A1828 " pdb=" N HIS A1828 " pdb=" CA HIS A1828 " pdb=" CB HIS A1828 " ideal model delta harmonic sigma weight residual -122.60 -137.27 14.67 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" CBQ AV0 A1902 " pdb=" CBT AV0 A1902 " pdb=" CCM AV0 A1902 " pdb=" OBV AV0 A1902 " ideal model delta sinusoidal sigma weight residual 306.95 131.31 175.64 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N HIS A1828 " pdb=" C HIS A1828 " pdb=" CA HIS A1828 " pdb=" CB HIS A1828 " ideal model delta harmonic sigma weight residual 122.80 133.85 -11.05 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1865 0.091 - 0.182: 169 0.182 - 0.273: 14 0.273 - 0.365: 0 0.365 - 0.456: 1 Chirality restraints: 2049 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.99e+01 chirality pdb=" CA HIS A1828 " pdb=" N HIS A1828 " pdb=" C HIS A1828 " pdb=" CB HIS A1828 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA LYS A1082 " pdb=" N LYS A1082 " pdb=" C LYS A1082 " pdb=" CB LYS A1082 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2046 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG B 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.104 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.306 2.00e-02 2.50e+03 2.64e-01 8.71e+02 pdb=" C7 NAG B 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.008 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A1907 " -0.171 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" C22 ERG A1907 " 0.166 2.00e-02 2.50e+03 pdb=" C23 ERG A1907 " 0.180 2.00e-02 2.50e+03 pdb=" C24 ERG A1907 " -0.174 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1723 2.75 - 3.29: 12534 3.29 - 3.83: 20706 3.83 - 4.36: 24400 4.36 - 4.90: 42597 Nonbonded interactions: 101960 Sorted by model distance: nonbonded pdb=" OG1 THR A 659 " pdb=" OG1 THR A1590 " model vdw 2.216 3.040 nonbonded pdb=" O TYR A 491 " pdb=" OG SER A 495 " model vdw 2.255 3.040 nonbonded pdb=" NH1 ARG A1435 " pdb=" OD2 ASP A1502 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR A 843 " pdb=" O ARG A1094 " model vdw 2.279 3.040 nonbonded pdb=" CD1 ILE A 675 " pdb=" C21 ERG A1909 " model vdw 2.288 3.880 ... (remaining 101955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.008 0.623 13381 Z= 0.669 Angle : 0.850 10.028 18224 Z= 0.547 Chirality : 0.052 0.456 2049 Planarity : 0.012 0.302 2187 Dihedral : 18.756 175.643 5817 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.22 % Allowed : 14.29 % Favored : 85.49 % Cbeta Deviations : 0.07 % 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: -0.29 (0.22), residues: 1495 helix: 0.70 (0.18), residues: 896 sheet: 0.45 (0.72), residues: 48 loop : -1.73 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 657 TYR 0.011 0.001 TYR A1571 PHE 0.042 0.002 PHE A1484 TRP 0.018 0.002 TRP A1509 HIS 0.005 0.001 HIS A1828 Details of bonding type rmsd covalent geometry : bond 0.00601 (13375) covalent geometry : angle 0.84477 (18212) SS BOND : bond 0.01793 ( 3) SS BOND : angle 2.65509 ( 6) hydrogen bonds : bond 0.15373 ( 646) hydrogen bonds : angle 5.84935 ( 1893) Misc. bond : bond 0.62280 ( 1) link_BETA1-4 : bond 0.00053 ( 1) link_BETA1-4 : angle 0.37401 ( 3) link_NAG-ASN : bond 0.02751 ( 1) link_NAG-ASN : angle 6.76766 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1376 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7432 (tt0) outliers start: 3 outliers final: 3 residues processed: 172 average time/residue: 0.1158 time to fit residues: 29.3369 Evaluate side-chains 150 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 PHE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1829 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 ASN A1214 GLN A1492 HIS A1514 ASN A1516 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.178537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131777 restraints weight = 15520.751| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.94 r_work: 0.3502 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13381 Z= 0.141 Angle : 0.607 10.299 18224 Z= 0.300 Chirality : 0.042 0.341 2049 Planarity : 0.005 0.062 2187 Dihedral : 14.458 147.206 2885 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.80 % Allowed : 14.88 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1495 helix: 1.25 (0.18), residues: 895 sheet: 0.47 (0.71), residues: 48 loop : -1.48 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 657 TYR 0.018 0.001 TYR A1503 PHE 0.017 0.001 PHE A1657 TRP 0.024 0.002 TRP A1509 HIS 0.008 0.001 HIS A1238 Details of bonding type rmsd covalent geometry : bond 0.00309 (13375) covalent geometry : angle 0.60468 (18212) SS BOND : bond 0.00523 ( 3) SS BOND : angle 2.08266 ( 6) hydrogen bonds : bond 0.05459 ( 646) hydrogen bonds : angle 4.35491 ( 1893) Misc. bond : bond 0.00018 ( 1) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 2.67788 ( 3) link_NAG-ASN : bond 0.01248 ( 1) link_NAG-ASN : angle 1.33203 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 LYS cc_start: 0.7126 (mmmt) cc_final: 0.6778 (mppt) REVERT: A 993 MET cc_start: 0.8158 (tpp) cc_final: 0.7945 (tpp) REVERT: A 1438 PHE cc_start: 0.7564 (t80) cc_final: 0.7333 (t80) REVERT: A 1497 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6662 (mt-10) outliers start: 24 outliers final: 8 residues processed: 173 average time/residue: 0.1071 time to fit residues: 27.7352 Evaluate side-chains 158 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1497 GLU Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 700 ASN A 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.177629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.130793 restraints weight = 15734.948| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.97 r_work: 0.3496 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13381 Z= 0.133 Angle : 0.570 9.906 18224 Z= 0.280 Chirality : 0.040 0.247 2049 Planarity : 0.004 0.054 2187 Dihedral : 11.608 130.897 2883 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.69 % Allowed : 14.58 % Favored : 82.72 % 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: 0.69 (0.22), residues: 1495 helix: 1.52 (0.18), residues: 889 sheet: 0.39 (0.71), residues: 48 loop : -1.31 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1138 TYR 0.011 0.001 TYR A 662 PHE 0.020 0.001 PHE A1657 TRP 0.029 0.001 TRP A1509 HIS 0.006 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00296 (13375) covalent geometry : angle 0.56845 (18212) SS BOND : bond 0.01218 ( 3) SS BOND : angle 2.20784 ( 6) hydrogen bonds : bond 0.05077 ( 646) hydrogen bonds : angle 4.10005 ( 1893) Misc. bond : bond 0.00047 ( 1) link_BETA1-4 : bond 0.00527 ( 1) link_BETA1-4 : angle 1.72278 ( 3) link_NAG-ASN : bond 0.00240 ( 1) link_NAG-ASN : angle 0.72265 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 852 ARG cc_start: 0.7528 (mtp85) cc_final: 0.7148 (mmt-90) REVERT: A 1223 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 1312 MET cc_start: 0.8216 (mmt) cc_final: 0.7822 (mmt) REVERT: A 1389 ARG cc_start: 0.5633 (mmt-90) cc_final: 0.4959 (mmm160) REVERT: A 1438 PHE cc_start: 0.7639 (t80) cc_final: 0.7367 (t80) REVERT: A 1497 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: A 1799 LYS cc_start: 0.6453 (ttpt) cc_final: 0.6235 (tttp) outliers start: 36 outliers final: 17 residues processed: 177 average time/residue: 0.1049 time to fit residues: 27.7991 Evaluate side-chains 164 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1497 GLU Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 150 optimal weight: 0.0770 chunk 12 optimal weight: 3.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128078 restraints weight = 15734.291| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.94 r_work: 0.3451 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13381 Z= 0.162 Angle : 0.580 9.477 18224 Z= 0.290 Chirality : 0.042 0.276 2049 Planarity : 0.004 0.055 2187 Dihedral : 10.776 124.930 2883 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.84 % Allowed : 15.26 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1495 helix: 1.49 (0.18), residues: 888 sheet: 0.30 (0.72), residues: 48 loop : -1.22 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 788 TYR 0.013 0.001 TYR A1048 PHE 0.016 0.002 PHE A1657 TRP 0.030 0.001 TRP A1509 HIS 0.007 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00383 (13375) covalent geometry : angle 0.57880 (18212) SS BOND : bond 0.00454 ( 3) SS BOND : angle 1.94666 ( 6) hydrogen bonds : bond 0.05434 ( 646) hydrogen bonds : angle 4.14405 ( 1893) Misc. bond : bond 0.00149 ( 1) link_BETA1-4 : bond 0.00087 ( 1) link_BETA1-4 : angle 2.08053 ( 3) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 0.60435 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 852 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7248 (mmt-90) REVERT: A 1223 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7147 (mp) REVERT: A 1327 MET cc_start: 0.8663 (mmm) cc_final: 0.7708 (mtm) REVERT: A 1389 ARG cc_start: 0.5601 (mmt-90) cc_final: 0.4921 (mmm160) REVERT: A 1497 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6714 (mt-10) REVERT: A 1799 LYS cc_start: 0.6475 (ttpt) cc_final: 0.6232 (tttp) outliers start: 38 outliers final: 26 residues processed: 174 average time/residue: 0.1043 time to fit residues: 26.9583 Evaluate side-chains 170 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1497 GLU Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 132 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.177732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131245 restraints weight = 15682.990| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.92 r_work: 0.3502 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13381 Z= 0.110 Angle : 0.522 9.434 18224 Z= 0.260 Chirality : 0.039 0.263 2049 Planarity : 0.004 0.052 2187 Dihedral : 10.156 117.305 2883 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 16.83 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.23), residues: 1495 helix: 1.72 (0.18), residues: 890 sheet: -0.16 (0.68), residues: 58 loop : -1.20 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.010 0.001 TYR A1503 PHE 0.022 0.001 PHE A1438 TRP 0.033 0.001 TRP A1509 HIS 0.006 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00233 (13375) covalent geometry : angle 0.52131 (18212) SS BOND : bond 0.00404 ( 3) SS BOND : angle 1.72431 ( 6) hydrogen bonds : bond 0.04495 ( 646) hydrogen bonds : angle 3.93937 ( 1893) Misc. bond : bond 0.00068 ( 1) link_BETA1-4 : bond 0.00141 ( 1) link_BETA1-4 : angle 1.56818 ( 3) link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 0.40777 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 778 HIS cc_start: 0.6568 (m-70) cc_final: 0.6268 (m-70) REVERT: A 852 ARG cc_start: 0.7597 (mtp85) cc_final: 0.7226 (mmt-90) REVERT: A 1327 MET cc_start: 0.8631 (mmm) cc_final: 0.7701 (mtm) REVERT: A 1389 ARG cc_start: 0.5632 (mmt-90) cc_final: 0.4969 (mmm160) outliers start: 32 outliers final: 20 residues processed: 173 average time/residue: 0.1058 time to fit residues: 27.1677 Evaluate side-chains 167 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1844 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 142 optimal weight: 0.8980 chunk 81 optimal weight: 0.0010 chunk 144 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.175866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129307 restraints weight = 15552.162| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.88 r_work: 0.3479 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13381 Z= 0.137 Angle : 0.542 9.447 18224 Z= 0.271 Chirality : 0.041 0.270 2049 Planarity : 0.004 0.049 2187 Dihedral : 10.065 116.173 2883 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.29 % Allowed : 16.08 % Favored : 80.63 % 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: 0.90 (0.23), residues: 1495 helix: 1.72 (0.18), residues: 887 sheet: -0.17 (0.68), residues: 58 loop : -1.22 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1065 TYR 0.011 0.001 TYR A1276 PHE 0.035 0.002 PHE A1438 TRP 0.032 0.001 TRP A1509 HIS 0.005 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00318 (13375) covalent geometry : angle 0.54059 (18212) SS BOND : bond 0.00396 ( 3) SS BOND : angle 1.72227 ( 6) hydrogen bonds : bond 0.04911 ( 646) hydrogen bonds : angle 3.96577 ( 1893) Misc. bond : bond 0.00121 ( 1) link_BETA1-4 : bond 0.00014 ( 1) link_BETA1-4 : angle 1.78597 ( 3) link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 0.71336 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.8005 (tp) REVERT: A 778 HIS cc_start: 0.6673 (m-70) cc_final: 0.6355 (m-70) REVERT: A 852 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7245 (mmt-90) REVERT: A 1223 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7178 (mp) REVERT: A 1327 MET cc_start: 0.8677 (mmm) cc_final: 0.7725 (mtm) REVERT: A 1389 ARG cc_start: 0.5646 (mmt-90) cc_final: 0.4980 (mmm160) outliers start: 44 outliers final: 29 residues processed: 183 average time/residue: 0.1036 time to fit residues: 28.4589 Evaluate side-chains 181 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1844 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126692 restraints weight = 15678.493| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.86 r_work: 0.3452 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13381 Z= 0.170 Angle : 0.588 9.415 18224 Z= 0.293 Chirality : 0.042 0.278 2049 Planarity : 0.004 0.049 2187 Dihedral : 10.062 117.251 2883 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.92 % Allowed : 16.45 % Favored : 80.63 % 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: 0.77 (0.22), residues: 1495 helix: 1.64 (0.18), residues: 880 sheet: -0.23 (0.68), residues: 58 loop : -1.28 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1065 TYR 0.014 0.001 TYR A1276 PHE 0.032 0.002 PHE A1438 TRP 0.030 0.002 TRP A1509 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00405 (13375) covalent geometry : angle 0.58617 (18212) SS BOND : bond 0.00427 ( 3) SS BOND : angle 1.73081 ( 6) hydrogen bonds : bond 0.05477 ( 646) hydrogen bonds : angle 4.05809 ( 1893) Misc. bond : bond 0.00161 ( 1) link_BETA1-4 : bond 0.00073 ( 1) link_BETA1-4 : angle 2.06079 ( 3) link_NAG-ASN : bond 0.00249 ( 1) link_NAG-ASN : angle 1.08545 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 852 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7268 (mmt-90) REVERT: A 872 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7186 (tt) REVERT: A 1221 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6131 (tp30) REVERT: A 1327 MET cc_start: 0.8785 (mmm) cc_final: 0.7807 (mtm) REVERT: A 1389 ARG cc_start: 0.5613 (mmt-90) cc_final: 0.4959 (mmm160) REVERT: A 1457 MET cc_start: 0.8713 (tpp) cc_final: 0.8477 (mmm) outliers start: 39 outliers final: 31 residues processed: 178 average time/residue: 0.1065 time to fit residues: 28.4310 Evaluate side-chains 178 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 824 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128545 restraints weight = 15573.875| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.87 r_work: 0.3471 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13381 Z= 0.131 Angle : 0.554 9.440 18224 Z= 0.276 Chirality : 0.041 0.272 2049 Planarity : 0.004 0.048 2187 Dihedral : 9.897 117.794 2883 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 16.60 % Favored : 80.40 % 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: 0.91 (0.22), residues: 1495 helix: 1.72 (0.18), residues: 887 sheet: 0.18 (0.74), residues: 48 loop : -1.22 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1065 TYR 0.010 0.001 TYR A1276 PHE 0.027 0.002 PHE A1438 TRP 0.039 0.001 TRP A1509 HIS 0.003 0.001 HIS A1828 Details of bonding type rmsd covalent geometry : bond 0.00297 (13375) covalent geometry : angle 0.55295 (18212) SS BOND : bond 0.00383 ( 3) SS BOND : angle 1.64256 ( 6) hydrogen bonds : bond 0.04913 ( 646) hydrogen bonds : angle 3.95522 ( 1893) Misc. bond : bond 0.00105 ( 1) link_BETA1-4 : bond 0.00008 ( 1) link_BETA1-4 : angle 1.81662 ( 3) link_NAG-ASN : bond 0.00140 ( 1) link_NAG-ASN : angle 0.85046 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7987 (tp) REVERT: A 488 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7362 (tt) REVERT: A 778 HIS cc_start: 0.6825 (m-70) cc_final: 0.6505 (m-70) REVERT: A 852 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7224 (mmt-90) REVERT: A 872 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7139 (tt) REVERT: A 877 LYS cc_start: 0.7614 (mtmm) cc_final: 0.7037 (mtmm) REVERT: A 979 PHE cc_start: 0.7752 (m-80) cc_final: 0.7483 (m-80) REVERT: A 1221 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6047 (tp30) REVERT: A 1327 MET cc_start: 0.8777 (mmm) cc_final: 0.7818 (mtm) REVERT: A 1389 ARG cc_start: 0.5601 (mmt-90) cc_final: 0.4949 (mmm160) outliers start: 40 outliers final: 28 residues processed: 177 average time/residue: 0.1063 time to fit residues: 27.8766 Evaluate side-chains 176 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1218 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.126333 restraints weight = 15721.342| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.84 r_work: 0.3447 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13381 Z= 0.184 Angle : 0.596 9.383 18224 Z= 0.298 Chirality : 0.042 0.278 2049 Planarity : 0.004 0.047 2187 Dihedral : 9.983 118.162 2883 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.84 % Allowed : 16.68 % Favored : 80.48 % 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: 0.73 (0.22), residues: 1495 helix: 1.59 (0.18), residues: 886 sheet: -0.29 (0.71), residues: 58 loop : -1.29 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1065 TYR 0.014 0.001 TYR A1276 PHE 0.024 0.002 PHE A1438 TRP 0.039 0.002 TRP A1509 HIS 0.004 0.001 HIS A1828 Details of bonding type rmsd covalent geometry : bond 0.00446 (13375) covalent geometry : angle 0.59478 (18212) SS BOND : bond 0.00420 ( 3) SS BOND : angle 1.69497 ( 6) hydrogen bonds : bond 0.05497 ( 646) hydrogen bonds : angle 4.06832 ( 1893) Misc. bond : bond 0.00168 ( 1) link_BETA1-4 : bond 0.00047 ( 1) link_BETA1-4 : angle 2.14456 ( 3) link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.13651 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (tp) REVERT: A 852 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7245 (mmt-90) REVERT: A 872 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7197 (tt) REVERT: A 877 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7105 (mtmm) REVERT: A 1223 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 1327 MET cc_start: 0.8834 (mmm) cc_final: 0.7836 (mtm) REVERT: A 1389 ARG cc_start: 0.5619 (mmt-90) cc_final: 0.4966 (mmm160) outliers start: 38 outliers final: 29 residues processed: 170 average time/residue: 0.1051 time to fit residues: 26.8726 Evaluate side-chains 172 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.174883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128045 restraints weight = 15752.904| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.82 r_work: 0.3468 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13381 Z= 0.145 Angle : 0.574 10.843 18224 Z= 0.285 Chirality : 0.041 0.271 2049 Planarity : 0.004 0.048 2187 Dihedral : 9.797 118.427 2883 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 16.68 % Favored : 80.48 % 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: 0.84 (0.22), residues: 1495 helix: 1.65 (0.18), residues: 893 sheet: 0.07 (0.76), residues: 48 loop : -1.24 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1065 TYR 0.011 0.001 TYR A1276 PHE 0.026 0.002 PHE A1438 TRP 0.041 0.002 TRP A1509 HIS 0.004 0.001 HIS A1828 Details of bonding type rmsd covalent geometry : bond 0.00338 (13375) covalent geometry : angle 0.57307 (18212) SS BOND : bond 0.00375 ( 3) SS BOND : angle 1.57574 ( 6) hydrogen bonds : bond 0.05081 ( 646) hydrogen bonds : angle 3.99977 ( 1893) Misc. bond : bond 0.00123 ( 1) link_BETA1-4 : bond 0.00025 ( 1) link_BETA1-4 : angle 1.91199 ( 3) link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 0.97317 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7989 (tp) REVERT: A 852 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7234 (mmt-90) REVERT: A 872 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7174 (tt) REVERT: A 877 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7099 (mtmm) REVERT: A 1019 GLU cc_start: 0.7257 (tp30) cc_final: 0.6809 (tp30) REVERT: A 1223 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7219 (mp) REVERT: A 1327 MET cc_start: 0.8809 (mmm) cc_final: 0.7810 (mtm) REVERT: A 1389 ARG cc_start: 0.5641 (mmt-90) cc_final: 0.4995 (mmm160) outliers start: 38 outliers final: 30 residues processed: 171 average time/residue: 0.1076 time to fit residues: 27.4785 Evaluate side-chains 174 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1829 ILE Chi-restraints excluded: chain A residue 1851 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 142 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.175284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128322 restraints weight = 15607.581| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.84 r_work: 0.3471 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13381 Z= 0.135 Angle : 0.570 11.508 18224 Z= 0.282 Chirality : 0.041 0.268 2049 Planarity : 0.004 0.048 2187 Dihedral : 9.724 117.965 2883 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.84 % Allowed : 16.75 % Favored : 80.40 % 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: 0.86 (0.22), residues: 1495 helix: 1.65 (0.18), residues: 899 sheet: 0.06 (0.76), residues: 48 loop : -1.23 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1065 TYR 0.011 0.001 TYR A1503 PHE 0.026 0.002 PHE A1438 TRP 0.041 0.002 TRP A1509 HIS 0.003 0.001 HIS A1828 Details of bonding type rmsd covalent geometry : bond 0.00309 (13375) covalent geometry : angle 0.56867 (18212) SS BOND : bond 0.00373 ( 3) SS BOND : angle 1.59367 ( 6) hydrogen bonds : bond 0.04963 ( 646) hydrogen bonds : angle 3.97375 ( 1893) Misc. bond : bond 0.00108 ( 1) link_BETA1-4 : bond 0.00079 ( 1) link_BETA1-4 : angle 1.87388 ( 3) link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 0.91632 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.85 seconds wall clock time: 51 minutes 59.32 seconds (3119.32 seconds total)