Starting phenix.real_space_refine on Thu Jul 31 19:36:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzn_36748/07_2025/8jzn_36748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzn_36748/07_2025/8jzn_36748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzn_36748/07_2025/8jzn_36748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzn_36748/07_2025/8jzn_36748.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzn_36748/07_2025/8jzn_36748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzn_36748/07_2025/8jzn_36748.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.094 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 2 5.49 5 S 72 5.16 5 C 8520 2.51 5 N 2042 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12831 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1489, 12155 Classifications: {'peptide': 1489} Link IDs: {'PTRANS': 66, 'TRANS': 1422} Chain breaks: 13 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 648 Unusual residues: {'AV0': 2, 'ERG': 14, 'POV': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Time building chain proxies: 8.03, per 1000 atoms: 0.63 Number of scatterers: 12831 At special positions: 0 Unit cell: (100.244, 117.127, 135.066, 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 72 16.00 P 2 15.00 O 2195 8.00 N 2042 7.00 C 8520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A1849 " Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 3 sheets defined 67.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 197 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.764A pdb=" N LYS A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.560A pdb=" N GLN A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.511A pdb=" N LEU A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.981A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.713A pdb=" N ARG A 422 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR A 423 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 424 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.696A pdb=" N HIS A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 removed outlier: 3.663A pdb=" N MET A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.505A pdb=" N TYR A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 497 removed outlier: 4.060A pdb=" N LYS A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 515 removed outlier: 4.061A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 559 through 583 removed outlier: 4.736A pdb=" N VAL A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 615 through 639 removed outlier: 3.587A pdb=" N TRP A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 671 through 711 removed outlier: 3.608A pdb=" N ILE A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.761A pdb=" N ILE A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.543A pdb=" N TYR A 731 " --> pdb=" O PRO A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 764 removed outlier: 3.737A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 removed outlier: 3.906A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.992A pdb=" N GLN A 799 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 826 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.556A pdb=" N GLN A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 899 Processing helix chain 'A' and resid 933 through 945 removed outlier: 3.596A pdb=" N THR A 939 " --> pdb=" O TYR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.563A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 971 Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.556A pdb=" N PHE A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.520A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1081 through 1089 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 1138 through 1142 Processing helix chain 'A' and resid 1172 through 1187 removed outlier: 3.993A pdb=" N THR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG A1182 " --> pdb=" O THR A1178 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 removed outlier: 3.547A pdb=" N THR A1206 " --> pdb=" O THR A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1232 Processing helix chain 'A' and resid 1267 through 1271 removed outlier: 3.927A pdb=" N MET A1270 " --> pdb=" O GLY A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1280 removed outlier: 3.661A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.531A pdb=" N THR A1289 " --> pdb=" O ASP A1285 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A1294 " --> pdb=" O PHE A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1325 removed outlier: 3.625A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'A' and resid 1384 through 1397 removed outlier: 3.768A pdb=" N GLN A1388 " --> pdb=" O TRP A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1445 removed outlier: 4.119A pdb=" N SER A1443 " --> pdb=" O SER A1439 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1467 Processing helix chain 'A' and resid 1471 through 1485 removed outlier: 4.171A pdb=" N PHE A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1512 removed outlier: 3.610A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A1501 " --> pdb=" O GLU A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1565 Processing helix chain 'A' and resid 1565 through 1583 Processing helix chain 'A' and resid 1597 through 1623 removed outlier: 3.813A pdb=" N ARG A1601 " --> pdb=" O ASN A1597 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A1602 " --> pdb=" O SER A1598 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A1608 " --> pdb=" O ILE A1604 " (cutoff:3.500A) Proline residue: A1609 - end of helix removed outlier: 3.698A pdb=" N LEU A1617 " --> pdb=" O ASN A1613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A1619 " --> pdb=" O GLY A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1665 removed outlier: 3.645A pdb=" N ILE A1645 " --> pdb=" O VAL A1641 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A1646 " --> pdb=" O MET A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1694 removed outlier: 3.652A pdb=" N ILE A1674 " --> pdb=" O VAL A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1753 removed outlier: 3.739A pdb=" N GLU A1729 " --> pdb=" O GLN A1725 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1730 " --> pdb=" O PRO A1726 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A1736 " --> pdb=" O ALA A1732 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A1738 " --> pdb=" O VAL A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1759 removed outlier: 3.778A pdb=" N ILE A1759 " --> pdb=" O LEU A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1763 through 1774 removed outlier: 4.276A pdb=" N MET A1770 " --> pdb=" O PHE A1766 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A1774 " --> pdb=" O MET A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1800 removed outlier: 3.949A pdb=" N ARG A1791 " --> pdb=" O LEU A1787 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1800 through 1821 removed outlier: 3.755A pdb=" N LEU A1806 " --> pdb=" O SER A1802 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A1815 " --> pdb=" O PHE A1811 " (cutoff:3.500A) Proline residue: A1818 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 removed outlier: 3.728A pdb=" N ARG A 376 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 781 Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1071 removed outlier: 3.759A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 843 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 12.749A pdb=" N VAL A1148 " --> pdb=" O HIS A1238 " (cutoff:3.500A) removed outlier: 15.753A pdb=" N GLU A1240 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 16.918A pdb=" N ILE A1150 " --> pdb=" O GLU A1240 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N TYR A1242 " --> pdb=" O ILE A1150 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLY A1152 " --> pdb=" O TYR A1242 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N CYS A1244 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG A1154 " --> pdb=" O CYS A1244 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS A1246 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR A1156 " --> pdb=" O LYS A1246 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1857 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: 4.73 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1892 1.31 - 1.43: 3698 1.43 - 1.56: 7258 1.56 - 1.68: 229 1.68 - 1.81: 126 Bond restraints: 13203 Sorted by residual: bond pdb=" C5 ERG A1912 " pdb=" C6 ERG A1912 " ideal model delta sigma weight residual 1.338 1.617 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C5 ERG A1908 " pdb=" C6 ERG A1908 " ideal model delta sigma weight residual 1.338 1.612 -0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C5 ERG A1913 " pdb=" C6 ERG A1913 " ideal model delta sigma weight residual 1.338 1.612 -0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C5 ERG A1915 " pdb=" C6 ERG A1915 " ideal model delta sigma weight residual 1.338 1.611 -0.273 2.00e-02 2.50e+03 1.86e+02 bond pdb=" C5 ERG A1906 " pdb=" C6 ERG A1906 " ideal model delta sigma weight residual 1.338 1.611 -0.273 2.00e-02 2.50e+03 1.86e+02 ... (remaining 13198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 17289 2.66 - 5.33: 518 5.33 - 7.99: 115 7.99 - 10.65: 45 10.65 - 13.32: 11 Bond angle restraints: 17978 Sorted by residual: angle pdb=" N VAL A 705 " pdb=" CA VAL A 705 " pdb=" C VAL A 705 " ideal model delta sigma weight residual 111.90 107.98 3.92 8.10e-01 1.52e+00 2.34e+01 angle pdb=" C14 ERG A1917 " pdb=" C8 ERG A1917 " pdb=" C9 ERG A1917 " ideal model delta sigma weight residual 116.25 102.93 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C14 ERG A1904 " pdb=" C8 ERG A1904 " pdb=" C9 ERG A1904 " ideal model delta sigma weight residual 116.25 103.29 12.96 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C14 ERG A1909 " pdb=" C8 ERG A1909 " pdb=" C9 ERG A1909 " ideal model delta sigma weight residual 116.25 103.98 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" N MET A 458 " pdb=" CA MET A 458 " pdb=" C MET A 458 " ideal model delta sigma weight residual 111.14 115.49 -4.35 1.08e+00 8.57e-01 1.62e+01 ... (remaining 17973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 8138 34.37 - 68.74: 434 68.74 - 103.11: 64 103.11 - 137.48: 26 137.48 - 171.85: 3 Dihedral angle restraints: 8665 sinusoidal: 4292 harmonic: 4373 Sorted by residual: dihedral pdb=" CA HIS A1826 " pdb=" C HIS A1826 " pdb=" N LYS A1827 " pdb=" CA LYS A1827 " ideal model delta harmonic sigma weight residual -180.00 -151.86 -28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ALA A 525 " pdb=" C ALA A 525 " pdb=" N GLN A 526 " pdb=" CA GLN A 526 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A1340 " pdb=" C LEU A1340 " pdb=" N VAL A1341 " pdb=" CA VAL A1341 " ideal model delta harmonic sigma weight residual 180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 8662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1924 0.125 - 0.250: 59 0.250 - 0.375: 16 0.375 - 0.500: 6 0.500 - 0.625: 19 Chirality restraints: 2024 Sorted by residual: chirality pdb=" C13 ERG A1905 " pdb=" C12 ERG A1905 " pdb=" C14 ERG A1905 " pdb=" C17 ERG A1905 " both_signs ideal model delta sigma weight residual False -2.93 -2.30 -0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" C13 ERG A1911 " pdb=" C12 ERG A1911 " pdb=" C14 ERG A1911 " pdb=" C17 ERG A1911 " both_signs ideal model delta sigma weight residual False -2.93 -2.30 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" C13 ERG A1916 " pdb=" C12 ERG A1916 " pdb=" C14 ERG A1916 " pdb=" C17 ERG A1916 " both_signs ideal model delta sigma weight residual False -2.93 -2.31 -0.62 2.00e-01 2.50e+01 9.58e+00 ... (remaining 2021 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1036 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO A1037 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1037 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1037 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1775 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A1776 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A1776 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1776 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 545 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " -0.031 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 37 2.41 - 3.03: 7321 3.03 - 3.65: 18792 3.65 - 4.28: 30717 4.28 - 4.90: 49456 Nonbonded interactions: 106323 Sorted by model distance: nonbonded pdb=" OAI AV0 A1902 " pdb=" OAS AV0 A1902 " model vdw 1.784 3.040 nonbonded pdb=" OG1 THR A1040 " pdb=" OE1 GLU A1043 " model vdw 2.199 3.040 nonbonded pdb=" O4 AV0 A1902 " pdb=" OAQ AV0 A1902 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU A 984 " pdb=" NH1 ARG A 988 " model vdw 2.207 3.120 nonbonded pdb=" OE1 GLU A 661 " pdb=" OG SER A1598 " model vdw 2.216 3.040 ... (remaining 106318 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: 1.130 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.019 0.279 13207 Z= 0.929 Angle : 1.122 13.317 17988 Z= 0.472 Chirality : 0.084 0.625 2024 Planarity : 0.005 0.067 2147 Dihedral : 21.229 171.849 5831 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.91 % Allowed : 16.42 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.20), residues: 1461 helix: -1.58 (0.15), residues: 863 sheet: -0.39 (0.57), residues: 76 loop : -0.77 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 493 HIS 0.010 0.001 HIS A1195 PHE 0.027 0.002 PHE A1657 TYR 0.017 0.002 TYR A1804 ARG 0.021 0.001 ARG A 791 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 1) link_NAG-ASN : angle 2.54639 ( 3) link_BETA1-4 : bond 0.00487 ( 1) link_BETA1-4 : angle 3.09471 ( 3) hydrogen bonds : bond 0.25260 ( 640) hydrogen bonds : angle 8.66458 ( 1857) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.74026 ( 4) covalent geometry : bond 0.01889 (13203) covalent geometry : angle 1.12131 (17978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.304 Fit side-chains REVERT: A 601 VAL cc_start: 0.8113 (t) cc_final: 0.7873 (m) REVERT: A 745 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7718 (mptt) REVERT: A 763 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7022 (mtm-85) REVERT: A 791 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.6985 (ptm-80) REVERT: A 1202 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8544 (m) REVERT: A 1770 MET cc_start: 0.6790 (mpt) cc_final: 0.5661 (mmp) outliers start: 25 outliers final: 17 residues processed: 167 average time/residue: 1.3751 time to fit residues: 251.1435 Evaluate side-chains 164 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1154 ARG Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1752 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 459 HIS A 507 GLN A 721 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN A1388 GLN A1688 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106018 restraints weight = 14262.991| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.63 r_work: 0.3092 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13207 Z= 0.152 Angle : 0.674 9.874 17988 Z= 0.326 Chirality : 0.044 0.187 2024 Planarity : 0.005 0.055 2147 Dihedral : 15.947 167.590 2984 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.90 % Allowed : 15.28 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1461 helix: -0.07 (0.16), residues: 892 sheet: 0.43 (0.65), residues: 66 loop : -0.49 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 664 HIS 0.010 0.001 HIS A1195 PHE 0.017 0.002 PHE A1581 TYR 0.017 0.001 TYR A1503 ARG 0.008 0.000 ARG A 791 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 1.82270 ( 3) link_BETA1-4 : bond 0.00095 ( 1) link_BETA1-4 : angle 1.80930 ( 3) hydrogen bonds : bond 0.05244 ( 640) hydrogen bonds : angle 4.91365 ( 1857) SS BOND : bond 0.00385 ( 2) SS BOND : angle 0.50439 ( 4) covalent geometry : bond 0.00341 (13203) covalent geometry : angle 0.67366 (17978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8586 (mmmt) cc_final: 0.7765 (mmtt) REVERT: A 443 ARG cc_start: 0.7761 (mtm180) cc_final: 0.6237 (mtm110) REVERT: A 518 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8358 (m) REVERT: A 533 TRP cc_start: 0.7150 (t60) cc_final: 0.5486 (m100) REVERT: A 640 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 645 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7677 (ttm110) REVERT: A 725 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5633 (mtm180) REVERT: A 745 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7161 (mptt) REVERT: A 791 ARG cc_start: 0.7524 (ptp-110) cc_final: 0.6385 (ptm-80) REVERT: A 794 THR cc_start: 0.8418 (p) cc_final: 0.8123 (t) REVERT: A 809 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7085 (p90) REVERT: A 974 GLU cc_start: 0.7486 (pm20) cc_final: 0.7265 (pm20) REVERT: A 1088 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7041 (t70) REVERT: A 1202 THR cc_start: 0.8867 (t) cc_final: 0.8612 (m) REVERT: A 1269 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6235 (mm-40) REVERT: A 1642 MET cc_start: 0.6558 (tmm) cc_final: 0.5979 (pmm) REVERT: A 1739 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6978 (tp30) REVERT: A 1836 VAL cc_start: 0.8040 (m) cc_final: 0.7770 (p) outliers start: 38 outliers final: 11 residues processed: 181 average time/residue: 1.1829 time to fit residues: 235.7359 Evaluate side-chains 160 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105205 restraints weight = 14231.458| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.25 r_work: 0.3109 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13207 Z= 0.133 Angle : 0.603 9.784 17988 Z= 0.293 Chirality : 0.041 0.155 2024 Planarity : 0.004 0.053 2147 Dihedral : 13.851 172.272 2966 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.82 % Allowed : 15.81 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1461 helix: 0.61 (0.17), residues: 887 sheet: 0.50 (0.66), residues: 66 loop : -0.41 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 664 HIS 0.008 0.001 HIS A1195 PHE 0.015 0.001 PHE A1581 TYR 0.016 0.001 TYR A1503 ARG 0.008 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 1.78186 ( 3) link_BETA1-4 : bond 0.00148 ( 1) link_BETA1-4 : angle 1.94066 ( 3) hydrogen bonds : bond 0.04752 ( 640) hydrogen bonds : angle 4.53947 ( 1857) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.49598 ( 4) covalent geometry : bond 0.00298 (13203) covalent geometry : angle 0.60264 (17978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8588 (mmmt) cc_final: 0.7786 (mmtt) REVERT: A 443 ARG cc_start: 0.7790 (mtm180) cc_final: 0.6245 (mtm110) REVERT: A 518 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8388 (m) REVERT: A 533 TRP cc_start: 0.7220 (t60) cc_final: 0.5453 (m100) REVERT: A 640 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 719 TRP cc_start: 0.6854 (m100) cc_final: 0.6639 (m100) REVERT: A 745 LYS cc_start: 0.7606 (ttmt) cc_final: 0.7160 (mptt) REVERT: A 763 ARG cc_start: 0.7683 (mmt180) cc_final: 0.6646 (mtm-85) REVERT: A 791 ARG cc_start: 0.7490 (ptp-110) cc_final: 0.6425 (ptm-80) REVERT: A 794 THR cc_start: 0.8385 (p) cc_final: 0.8098 (t) REVERT: A 809 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6992 (p90) REVERT: A 974 GLU cc_start: 0.7500 (pm20) cc_final: 0.7298 (pm20) REVERT: A 1088 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7027 (t70) REVERT: A 1202 THR cc_start: 0.8888 (t) cc_final: 0.8610 (m) REVERT: A 1268 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: A 1269 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6316 (mm-40) REVERT: A 1690 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5963 (mtt) REVERT: A 1694 MET cc_start: 0.5494 (OUTLIER) cc_final: 0.4814 (mpt) REVERT: A 1836 VAL cc_start: 0.7776 (m) cc_final: 0.7489 (p) outliers start: 50 outliers final: 15 residues processed: 186 average time/residue: 1.2473 time to fit residues: 254.1713 Evaluate side-chains 169 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.155400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104138 restraints weight = 14193.508| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.80 r_work: 0.3066 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13207 Z= 0.192 Angle : 0.641 10.406 17988 Z= 0.314 Chirality : 0.043 0.173 2024 Planarity : 0.005 0.052 2147 Dihedral : 13.158 178.690 2965 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.59 % Allowed : 16.73 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1461 helix: 0.73 (0.17), residues: 883 sheet: 0.40 (0.65), residues: 66 loop : -0.50 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 625 HIS 0.008 0.001 HIS A1195 PHE 0.014 0.002 PHE A1581 TYR 0.018 0.002 TYR A1503 ARG 0.008 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 1.88267 ( 3) link_BETA1-4 : bond 0.00082 ( 1) link_BETA1-4 : angle 2.23118 ( 3) hydrogen bonds : bond 0.04927 ( 640) hydrogen bonds : angle 4.51355 ( 1857) SS BOND : bond 0.00386 ( 2) SS BOND : angle 0.47340 ( 4) covalent geometry : bond 0.00461 (13203) covalent geometry : angle 0.64043 (17978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7232 (mt) REVERT: A 386 LYS cc_start: 0.8576 (mmmt) cc_final: 0.7759 (mmtt) REVERT: A 443 ARG cc_start: 0.7779 (mtm180) cc_final: 0.6210 (mtm110) REVERT: A 518 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 533 TRP cc_start: 0.7233 (t60) cc_final: 0.5441 (m100) REVERT: A 640 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8119 (mp) REVERT: A 725 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5502 (mtm180) REVERT: A 745 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7096 (mptt) REVERT: A 763 ARG cc_start: 0.7518 (mmt180) cc_final: 0.6504 (mtm-85) REVERT: A 791 ARG cc_start: 0.7386 (ptp-110) cc_final: 0.6623 (ptt-90) REVERT: A 794 THR cc_start: 0.8376 (p) cc_final: 0.8019 (t) REVERT: A 809 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.6954 (p90) REVERT: A 974 GLU cc_start: 0.7485 (pm20) cc_final: 0.7188 (pm20) REVERT: A 1057 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7158 (tm-30) REVERT: A 1088 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7121 (t70) REVERT: A 1202 THR cc_start: 0.8804 (t) cc_final: 0.8547 (m) REVERT: A 1268 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: A 1269 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6181 (mm-40) REVERT: A 1642 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5822 (pmm) REVERT: A 1690 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5966 (mtt) REVERT: A 1694 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.4842 (mpt) REVERT: A 1836 VAL cc_start: 0.7756 (m) cc_final: 0.7463 (p) outliers start: 47 outliers final: 17 residues processed: 178 average time/residue: 1.2093 time to fit residues: 236.4373 Evaluate side-chains 179 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1642 MET Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 0.0270 chunk 55 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107709 restraints weight = 14278.121| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.79 r_work: 0.3117 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13207 Z= 0.108 Angle : 0.561 8.719 17988 Z= 0.276 Chirality : 0.039 0.159 2024 Planarity : 0.004 0.050 2147 Dihedral : 12.183 157.076 2963 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.60 % Allowed : 17.80 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1461 helix: 1.12 (0.17), residues: 886 sheet: 0.63 (0.66), residues: 66 loop : -0.44 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 625 HIS 0.009 0.001 HIS A1195 PHE 0.013 0.001 PHE A1581 TYR 0.017 0.001 TYR A1503 ARG 0.008 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 1) link_NAG-ASN : angle 1.66562 ( 3) link_BETA1-4 : bond 0.00187 ( 1) link_BETA1-4 : angle 1.86572 ( 3) hydrogen bonds : bond 0.04077 ( 640) hydrogen bonds : angle 4.28281 ( 1857) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.44114 ( 4) covalent geometry : bond 0.00235 (13203) covalent geometry : angle 0.56020 (17978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8574 (mmmt) cc_final: 0.7759 (mmtt) REVERT: A 443 ARG cc_start: 0.7766 (mtm180) cc_final: 0.6185 (mtm110) REVERT: A 518 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 533 TRP cc_start: 0.7301 (t60) cc_final: 0.5471 (m100) REVERT: A 725 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5492 (mtm180) REVERT: A 745 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7052 (mptt) REVERT: A 791 ARG cc_start: 0.7411 (ptp-110) cc_final: 0.6339 (ptm-80) REVERT: A 794 THR cc_start: 0.8307 (p) cc_final: 0.8042 (t) REVERT: A 862 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3361 (tpm170) REVERT: A 974 GLU cc_start: 0.7572 (pm20) cc_final: 0.7315 (pm20) REVERT: A 1057 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 1088 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7178 (t70) REVERT: A 1202 THR cc_start: 0.8837 (t) cc_final: 0.8604 (m) REVERT: A 1269 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6346 (mm-40) REVERT: A 1504 ARG cc_start: 0.7300 (tmm160) cc_final: 0.7097 (tmm160) REVERT: A 1642 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5502 (pmm) REVERT: A 1694 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4828 (mpt) REVERT: A 1836 VAL cc_start: 0.7708 (m) cc_final: 0.7431 (p) REVERT: A 1848 ASN cc_start: 0.7960 (p0) cc_final: 0.7720 (p0) outliers start: 34 outliers final: 15 residues processed: 170 average time/residue: 1.2358 time to fit residues: 231.1010 Evaluate side-chains 169 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1642 MET Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 721 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105723 restraints weight = 14326.396| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.82 r_work: 0.3092 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13207 Z= 0.134 Angle : 0.574 9.253 17988 Z= 0.283 Chirality : 0.040 0.158 2024 Planarity : 0.004 0.050 2147 Dihedral : 11.842 145.263 2963 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.13 % Allowed : 17.88 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1461 helix: 1.20 (0.17), residues: 886 sheet: 0.68 (0.67), residues: 66 loop : -0.41 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 625 HIS 0.007 0.001 HIS A1195 PHE 0.013 0.001 PHE A1581 TYR 0.018 0.001 TYR A1503 ARG 0.008 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 1) link_NAG-ASN : angle 1.75311 ( 3) link_BETA1-4 : bond 0.00117 ( 1) link_BETA1-4 : angle 1.93344 ( 3) hydrogen bonds : bond 0.04251 ( 640) hydrogen bonds : angle 4.26142 ( 1857) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.44728 ( 4) covalent geometry : bond 0.00312 (13203) covalent geometry : angle 0.57314 (17978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8566 (mmmt) cc_final: 0.7748 (mmtt) REVERT: A 443 ARG cc_start: 0.7782 (mtm180) cc_final: 0.6202 (mtm110) REVERT: A 518 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8406 (m) REVERT: A 533 TRP cc_start: 0.7321 (t60) cc_final: 0.5319 (m100) REVERT: A 725 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5502 (mtm180) REVERT: A 745 LYS cc_start: 0.7479 (ttmt) cc_final: 0.7031 (mptt) REVERT: A 791 ARG cc_start: 0.7426 (ptp-110) cc_final: 0.6341 (ptm-80) REVERT: A 794 THR cc_start: 0.8312 (p) cc_final: 0.8032 (t) REVERT: A 862 ARG cc_start: 0.4524 (OUTLIER) cc_final: 0.3203 (tpm170) REVERT: A 974 GLU cc_start: 0.7576 (pm20) cc_final: 0.7306 (pm20) REVERT: A 1057 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7087 (tm-30) REVERT: A 1088 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7245 (t70) REVERT: A 1202 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 1269 GLN cc_start: 0.7299 (mt0) cc_final: 0.6315 (mm-40) REVERT: A 1380 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.6002 (tt0) REVERT: A 1694 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4812 (mpt) REVERT: A 1836 VAL cc_start: 0.7706 (m) cc_final: 0.7431 (p) REVERT: A 1848 ASN cc_start: 0.7992 (p0) cc_final: 0.7715 (p0) outliers start: 41 outliers final: 21 residues processed: 179 average time/residue: 1.1981 time to fit residues: 235.7280 Evaluate side-chains 177 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102031 restraints weight = 14149.943| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.28 r_work: 0.3062 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13207 Z= 0.224 Angle : 0.653 11.080 17988 Z= 0.321 Chirality : 0.044 0.185 2024 Planarity : 0.005 0.050 2147 Dihedral : 11.960 139.083 2963 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.74 % Allowed : 17.72 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1461 helix: 0.97 (0.17), residues: 880 sheet: 0.50 (0.65), residues: 66 loop : -0.49 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 625 HIS 0.006 0.001 HIS A1195 PHE 0.016 0.002 PHE A1744 TYR 0.021 0.002 TYR A1503 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 2.01916 ( 3) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 2.27827 ( 3) hydrogen bonds : bond 0.04998 ( 640) hydrogen bonds : angle 4.44014 ( 1857) SS BOND : bond 0.00410 ( 2) SS BOND : angle 0.56748 ( 4) covalent geometry : bond 0.00540 (13203) covalent geometry : angle 0.65155 (17978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7078 (mt) REVERT: A 386 LYS cc_start: 0.8576 (mmmt) cc_final: 0.7747 (mmtt) REVERT: A 443 ARG cc_start: 0.7826 (mtm180) cc_final: 0.6198 (mtm110) REVERT: A 518 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8341 (m) REVERT: A 533 TRP cc_start: 0.7226 (t60) cc_final: 0.5439 (m100) REVERT: A 640 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 725 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5513 (mtm180) REVERT: A 745 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7053 (mptt) REVERT: A 791 ARG cc_start: 0.7352 (ptp-110) cc_final: 0.6507 (ptt-90) REVERT: A 794 THR cc_start: 0.8259 (p) cc_final: 0.7879 (t) REVERT: A 809 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6957 (p90) REVERT: A 862 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.3249 (tpm170) REVERT: A 974 GLU cc_start: 0.7523 (pm20) cc_final: 0.7222 (pm20) REVERT: A 1088 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.6970 (t70) REVERT: A 1202 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8466 (m) REVERT: A 1269 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6267 (mm-40) REVERT: A 1380 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5998 (tt0) REVERT: A 1694 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.4859 (mpt) REVERT: A 1836 VAL cc_start: 0.7775 (m) cc_final: 0.7479 (p) outliers start: 49 outliers final: 22 residues processed: 184 average time/residue: 1.2182 time to fit residues: 246.6916 Evaluate side-chains 184 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 23 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106970 restraints weight = 14244.115| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.83 r_work: 0.3115 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13207 Z= 0.114 Angle : 0.569 9.654 17988 Z= 0.281 Chirality : 0.040 0.163 2024 Planarity : 0.004 0.049 2147 Dihedral : 11.408 128.023 2963 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.60 % Allowed : 18.56 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1461 helix: 1.29 (0.18), residues: 882 sheet: 0.73 (0.67), residues: 66 loop : -0.38 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 625 HIS 0.008 0.001 HIS A1195 PHE 0.031 0.001 PHE A 548 TYR 0.015 0.001 TYR A1503 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 1) link_NAG-ASN : angle 1.63777 ( 3) link_BETA1-4 : bond 0.00301 ( 1) link_BETA1-4 : angle 1.93352 ( 3) hydrogen bonds : bond 0.04065 ( 640) hydrogen bonds : angle 4.22997 ( 1857) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.39043 ( 4) covalent geometry : bond 0.00249 (13203) covalent geometry : angle 0.56780 (17978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.6833 (tp30) cc_final: 0.6447 (pt0) REVERT: A 386 LYS cc_start: 0.8596 (mmmt) cc_final: 0.7763 (mmtt) REVERT: A 443 ARG cc_start: 0.7769 (mtm180) cc_final: 0.6178 (mtm110) REVERT: A 518 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8380 (m) REVERT: A 533 TRP cc_start: 0.7326 (t60) cc_final: 0.5337 (m100) REVERT: A 640 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 719 TRP cc_start: 0.6739 (m100) cc_final: 0.6506 (m100) REVERT: A 725 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5494 (mtm180) REVERT: A 745 LYS cc_start: 0.7395 (ttmt) cc_final: 0.6930 (mptt) REVERT: A 791 ARG cc_start: 0.7381 (ptp-110) cc_final: 0.6291 (ptm-80) REVERT: A 794 THR cc_start: 0.8340 (p) cc_final: 0.8048 (t) REVERT: A 862 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.3239 (tpm170) REVERT: A 974 GLU cc_start: 0.7550 (pm20) cc_final: 0.7195 (pm20) REVERT: A 1088 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7183 (t70) REVERT: A 1202 THR cc_start: 0.8895 (t) cc_final: 0.8608 (m) REVERT: A 1268 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6879 (tt0) REVERT: A 1269 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6477 (mm-40) REVERT: A 1388 GLN cc_start: 0.4931 (OUTLIER) cc_final: 0.4554 (mt0) REVERT: A 1694 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4762 (mpt) REVERT: A 1836 VAL cc_start: 0.7700 (m) cc_final: 0.7442 (p) REVERT: A 1848 ASN cc_start: 0.7972 (p0) cc_final: 0.7766 (p0) outliers start: 34 outliers final: 18 residues processed: 171 average time/residue: 1.7314 time to fit residues: 328.3384 Evaluate side-chains 173 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1388 GLN Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1816 ILE Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105256 restraints weight = 14183.116| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.50 r_work: 0.3084 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13207 Z= 0.184 Angle : 0.613 10.361 17988 Z= 0.303 Chirality : 0.042 0.167 2024 Planarity : 0.004 0.050 2147 Dihedral : 11.472 125.048 2963 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.83 % Allowed : 18.33 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1461 helix: 1.13 (0.17), residues: 884 sheet: 0.64 (0.66), residues: 66 loop : -0.38 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 625 HIS 0.006 0.001 HIS A1195 PHE 0.026 0.002 PHE A 548 TYR 0.020 0.002 TYR A1503 ARG 0.004 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.87690 ( 3) link_BETA1-4 : bond 0.00057 ( 1) link_BETA1-4 : angle 2.12291 ( 3) hydrogen bonds : bond 0.04601 ( 640) hydrogen bonds : angle 4.31703 ( 1857) SS BOND : bond 0.00366 ( 2) SS BOND : angle 0.53100 ( 4) covalent geometry : bond 0.00443 (13203) covalent geometry : angle 0.61164 (17978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 2.591 Fit side-chains REVERT: A 386 LYS cc_start: 0.8615 (mmmt) cc_final: 0.7787 (mmtt) REVERT: A 443 ARG cc_start: 0.7867 (mtm180) cc_final: 0.6270 (mtm110) REVERT: A 518 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8417 (m) REVERT: A 533 TRP cc_start: 0.7339 (t60) cc_final: 0.5526 (m100) REVERT: A 640 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 720 ARG cc_start: 0.6158 (mpp-170) cc_final: 0.5207 (mtt-85) REVERT: A 725 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5551 (mtm180) REVERT: A 745 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7020 (mptt) REVERT: A 791 ARG cc_start: 0.7458 (ptp-110) cc_final: 0.6367 (ptm-80) REVERT: A 794 THR cc_start: 0.8415 (p) cc_final: 0.8091 (t) REVERT: A 809 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7116 (p90) REVERT: A 862 ARG cc_start: 0.4532 (OUTLIER) cc_final: 0.3254 (tpm170) REVERT: A 974 GLU cc_start: 0.7560 (pm20) cc_final: 0.7252 (pm20) REVERT: A 1088 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7171 (t70) REVERT: A 1202 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8603 (m) REVERT: A 1268 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6971 (tt0) REVERT: A 1269 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6513 (mm-40) REVERT: A 1694 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.4745 (mpt) REVERT: A 1836 VAL cc_start: 0.7749 (m) cc_final: 0.7477 (p) REVERT: A 1848 ASN cc_start: 0.8033 (p0) cc_final: 0.7767 (p0) outliers start: 37 outliers final: 21 residues processed: 169 average time/residue: 1.6613 time to fit residues: 309.5324 Evaluate side-chains 177 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1816 ILE Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 145 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106647 restraints weight = 14173.372| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.64 r_work: 0.3105 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13207 Z= 0.129 Angle : 0.576 9.388 17988 Z= 0.285 Chirality : 0.040 0.153 2024 Planarity : 0.004 0.049 2147 Dihedral : 11.233 119.999 2963 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.37 % Allowed : 18.72 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1461 helix: 1.29 (0.18), residues: 882 sheet: 0.75 (0.67), residues: 66 loop : -0.36 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 625 HIS 0.009 0.001 HIS A1195 PHE 0.028 0.001 PHE A 548 TYR 0.019 0.001 TYR A1503 ARG 0.009 0.000 ARG A 852 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 1.70763 ( 3) link_BETA1-4 : bond 0.00151 ( 1) link_BETA1-4 : angle 1.94784 ( 3) hydrogen bonds : bond 0.04208 ( 640) hydrogen bonds : angle 4.22611 ( 1857) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.42060 ( 4) covalent geometry : bond 0.00295 (13203) covalent geometry : angle 0.57531 (17978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8616 (mmmt) cc_final: 0.7788 (mmtt) REVERT: A 443 ARG cc_start: 0.7847 (mtm180) cc_final: 0.6256 (mtm110) REVERT: A 518 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8430 (m) REVERT: A 533 TRP cc_start: 0.7378 (t60) cc_final: 0.5416 (m100) REVERT: A 640 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8107 (mp) REVERT: A 725 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5538 (mtm180) REVERT: A 745 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7000 (mptt) REVERT: A 791 ARG cc_start: 0.7427 (ptp-110) cc_final: 0.6333 (ptm-80) REVERT: A 794 THR cc_start: 0.8398 (p) cc_final: 0.8086 (t) REVERT: A 809 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7146 (p90) REVERT: A 862 ARG cc_start: 0.4581 (OUTLIER) cc_final: 0.3298 (tpm170) REVERT: A 974 GLU cc_start: 0.7564 (pm20) cc_final: 0.7197 (pm20) REVERT: A 1088 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.7212 (t70) REVERT: A 1182 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6314 (ttm110) REVERT: A 1202 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8627 (m) REVERT: A 1268 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7123 (tt0) REVERT: A 1269 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6305 (mm-40) REVERT: A 1694 MET cc_start: 0.5289 (OUTLIER) cc_final: 0.4783 (mpt) REVERT: A 1836 VAL cc_start: 0.7723 (m) cc_final: 0.7465 (p) REVERT: A 1848 ASN cc_start: 0.7976 (p0) cc_final: 0.7759 (p0) outliers start: 31 outliers final: 18 residues processed: 164 average time/residue: 1.9490 time to fit residues: 350.0600 Evaluate side-chains 178 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1816 ILE Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.0040 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 GLN A1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.156823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106117 restraints weight = 14172.212| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.50 r_work: 0.3096 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13207 Z= 0.158 Angle : 0.595 9.937 17988 Z= 0.294 Chirality : 0.041 0.161 2024 Planarity : 0.004 0.049 2147 Dihedral : 11.195 117.221 2961 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 18.41 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1461 helix: 1.24 (0.17), residues: 882 sheet: 0.29 (0.65), residues: 71 loop : -0.32 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 625 HIS 0.007 0.001 HIS A1195 PHE 0.026 0.002 PHE A 548 TYR 0.018 0.001 TYR A1503 ARG 0.005 0.000 ARG A 988 Details of bonding type rmsd link_NAG-ASN : bond 0.00000 ( 1) link_NAG-ASN : angle 1.79260 ( 3) link_BETA1-4 : bond 0.00018 ( 1) link_BETA1-4 : angle 2.04650 ( 3) hydrogen bonds : bond 0.04397 ( 640) hydrogen bonds : angle 4.25016 ( 1857) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.46926 ( 4) covalent geometry : bond 0.00375 (13203) covalent geometry : angle 0.59404 (17978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11998.42 seconds wall clock time: 212 minutes 25.70 seconds (12745.70 seconds total)