Starting phenix.real_space_refine on Sat Jul 4 13:16:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gju_51403/07_2026/9gju_51403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gju_51403/07_2026/9gju_51403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gju_51403/07_2026/9gju_51403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gju_51403/07_2026/9gju_51403.map" model { file = "/net/cci-nas-00/data/ceres_data/9gju_51403/07_2026/9gju_51403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gju_51403/07_2026/9gju_51403.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 24 5.49 5 Mg 1 5.21 5 S 120 5.16 5 C 13240 2.51 5 N 3554 2.21 5 O 3994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20935 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 806 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 935 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 840 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "G" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 16306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2020, 16306 Classifications: {'peptide': 2020} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 79, 'TRANS': 1940} Chain breaks: 9 Chain: "B" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1572 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11892 SG CYS A1236 57.496 32.459 44.726 1.00 37.24 S ATOM 11915 SG CYS A1239 59.020 30.390 47.635 1.00 50.80 S ATOM 11542 SG CYS A1191 77.663 33.779 37.022 1.00 41.61 S ATOM 13292 SG CYS A1428 73.588 32.941 36.868 1.00 54.19 S ATOM 13298 SG CYS A1429 75.417 35.747 38.947 1.00 39.23 S Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 20935 At special positions: 0 Unit cell: (126.768, 118.428, 192.654, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 120 16.00 P 24 15.00 Mg 1 11.99 O 3994 8.00 N 3554 7.00 C 13240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 931.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" NE2 HIS A1423 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A1421 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1239 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1236 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1428 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1429 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1191 " Number of angles added : 1 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4856 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 11 sheets defined 63.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.602A pdb=" N SER C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 504 removed outlier: 3.977A pdb=" N HIS C 502 " --> pdb=" O TYR C 498 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 541 removed outlier: 4.079A pdb=" N HIS C 535 " --> pdb=" O MET C 531 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 574 removed outlier: 3.954A pdb=" N SER C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 485 removed outlier: 3.544A pdb=" N SER D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 503 removed outlier: 3.586A pdb=" N HIS D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 541 removed outlier: 4.002A pdb=" N GLN D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 541 " --> pdb=" O GLU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 578 removed outlier: 3.570A pdb=" N LYS D 559 " --> pdb=" O ARG D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 4.298A pdb=" N LYS D 595 " --> pdb=" O PRO D 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 484 Processing helix chain 'E' and resid 489 through 503 Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 507 through 541 removed outlier: 3.559A pdb=" N LEU E 511 " --> pdb=" O ASP E 507 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 513 " --> pdb=" O GLU E 509 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS E 535 " --> pdb=" O MET E 531 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN E 539 " --> pdb=" O HIS E 535 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 573 Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.744A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.567A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.563A pdb=" N ASN A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.620A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.770A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.585A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 288 removed outlier: 4.061A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 325 removed outlier: 3.909A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.710A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.540A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 411 removed outlier: 3.872A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 487 removed outlier: 5.777A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.723A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 522 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.506A pdb=" N PHE A 579 " --> pdb=" O GLY A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.780A pdb=" N VAL A 585 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.825A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.636A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 760 " --> pdb=" O HIS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.673A pdb=" N THR A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 811 through 821 removed outlier: 3.826A pdb=" N PHE A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.998A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 972 through 981 Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.932A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1080 removed outlier: 4.389A pdb=" N ILE A1075 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 removed outlier: 3.925A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'A' and resid 1126 through 1136 Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1238 through 1242 removed outlier: 3.731A pdb=" N GLY A1242 " --> pdb=" O CYS A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1309 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1336 Processing helix chain 'A' and resid 1391 through 1407 Processing helix chain 'A' and resid 1482 through 1486 Processing helix chain 'A' and resid 1487 through 1511 Processing helix chain 'A' and resid 1515 through 1519 Processing helix chain 'A' and resid 1530 through 1537 removed outlier: 3.588A pdb=" N ILE A1536 " --> pdb=" O THR A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1554 Processing helix chain 'A' and resid 1554 through 1560 Processing helix chain 'A' and resid 1565 through 1579 Processing helix chain 'A' and resid 1581 through 1584 Processing helix chain 'A' and resid 1585 through 1594 removed outlier: 3.725A pdb=" N HIS A1594 " --> pdb=" O ASN A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1604 Processing helix chain 'A' and resid 1614 through 1618 removed outlier: 4.137A pdb=" N GLN A1618 " --> pdb=" O LEU A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1641 Processing helix chain 'A' and resid 1653 through 1676 removed outlier: 3.798A pdb=" N ILE A1657 " --> pdb=" O ASP A1653 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A1658 " --> pdb=" O GLU A1654 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU A1659 " --> pdb=" O THR A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1689 through 1708 Processing helix chain 'A' and resid 1709 through 1712 removed outlier: 4.533A pdb=" N ARG A1712 " --> pdb=" O THR A1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1709 through 1712' Processing helix chain 'A' and resid 1727 through 1743 Processing helix chain 'A' and resid 1780 through 1786 Processing helix chain 'A' and resid 1804 through 1810 Processing helix chain 'A' and resid 1818 through 1833 Proline residue: A1827 - end of helix removed outlier: 3.687A pdb=" N ARG A1831 " --> pdb=" O PRO A1827 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A1832 " --> pdb=" O LEU A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1857 removed outlier: 3.730A pdb=" N SER A1855 " --> pdb=" O LEU A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1891 Processing helix chain 'A' and resid 1895 through 1900 removed outlier: 3.680A pdb=" N LYS A1900 " --> pdb=" O THR A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1914 Processing helix chain 'A' and resid 1918 through 1929 Processing helix chain 'A' and resid 1948 through 1966 removed outlier: 3.512A pdb=" N ILE A1952 " --> pdb=" O ASN A1948 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1995 removed outlier: 4.074A pdb=" N TYR A1995 " --> pdb=" O MET A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2038 removed outlier: 3.531A pdb=" N VAL A2032 " --> pdb=" O PRO A2028 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS A2035 " --> pdb=" O LYS A2031 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A2036 " --> pdb=" O VAL A2032 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A2037 " --> pdb=" O LEU A2033 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A2038 " --> pdb=" O GLU A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2071 removed outlier: 3.660A pdb=" N GLN A2071 " --> pdb=" O LYS A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2083 through 2092 Processing helix chain 'A' and resid 2097 through 2107 Processing helix chain 'A' and resid 2113 through 2133 removed outlier: 3.775A pdb=" N LEU A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2172 Processing helix chain 'A' and resid 2177 through 2189 removed outlier: 3.656A pdb=" N TYR A2181 " --> pdb=" O SER A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2198 through 2205 Processing helix chain 'A' and resid 2206 through 2217 removed outlier: 3.615A pdb=" N GLY A2217 " --> pdb=" O ARG A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2242 removed outlier: 3.564A pdb=" N SER A2242 " --> pdb=" O ILE A2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 489 through 502 removed outlier: 4.745A pdb=" N ARG B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 541 removed outlier: 3.525A pdb=" N GLN B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 573 Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.603A pdb=" N SER B 607 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 609 " --> pdb=" O GLN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 657 through 672 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 385 through 388 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.590A pdb=" N ILE A 199 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 556 removed outlier: 5.223A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 830 removed outlier: 4.597A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1230 Processing sheet with id=AA8, first strand: chain 'A' and resid 1379 through 1381 removed outlier: 4.301A pdb=" N PHE A1379 " --> pdb=" O VAL A1386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1647 through 1650 Processing sheet with id=AB1, first strand: chain 'A' and resid 1775 through 1779 removed outlier: 6.579A pdb=" N PHE A1996 " --> pdb=" O LYS A2021 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS A2021 " --> pdb=" O PHE A1996 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN A2020 " --> pdb=" O GLY A1971 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLY A1971 " --> pdb=" O GLN A2020 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A1935 " --> pdb=" O LEU A1972 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A1974 " --> pdb=" O GLY A1935 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A1937 " --> pdb=" O VAL A1974 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N LYS A1976 " --> pdb=" O VAL A1937 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER A1939 " --> pdb=" O LYS A1976 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN A1838 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1936 " --> pdb=" O GLN A1838 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG A1839 " --> pdb=" O PHE A1863 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2191 through 2195 1170 hydrogen bonds defined for protein. 3363 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: 4.88 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6678 1.34 - 1.46: 3411 1.46 - 1.58: 11046 1.58 - 1.70: 44 1.70 - 1.82: 200 Bond restraints: 21379 Sorted by residual: bond pdb=" N ASP A1522 " pdb=" CA ASP A1522 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.60e+00 bond pdb=" C MET C 479 " pdb=" N PRO C 480 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.38e-02 5.25e+03 4.57e+00 bond pdb=" C ILE C 578 " pdb=" N PRO C 579 " ideal model delta sigma weight residual 1.341 1.370 -0.029 1.60e-02 3.91e+03 3.21e+00 bond pdb=" N PRO C 579 " pdb=" CA PRO C 579 " ideal model delta sigma weight residual 1.466 1.492 -0.026 1.50e-02 4.44e+03 3.03e+00 bond pdb=" C ILE A1521 " pdb=" N ASP A1522 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.37e-02 5.33e+03 2.38e+00 ... (remaining 21374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 28778 2.18 - 4.36: 189 4.36 - 6.54: 27 6.54 - 8.72: 2 8.72 - 10.90: 1 Bond angle restraints: 28997 Sorted by residual: angle pdb=" CB MET B 577 " pdb=" CG MET B 577 " pdb=" SD MET B 577 " ideal model delta sigma weight residual 112.70 123.60 -10.90 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C VAL A1966 " pdb=" CA VAL A1966 " pdb=" CB VAL A1966 " ideal model delta sigma weight residual 112.16 107.46 4.70 1.63e+00 3.76e-01 8.33e+00 angle pdb=" CB GLN A2030 " pdb=" CG GLN A2030 " pdb=" CD GLN A2030 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.70e+00 3.46e-01 7.72e+00 angle pdb=" N TRP A 915 " pdb=" CA TRP A 915 " pdb=" C TRP A 915 " ideal model delta sigma weight residual 107.20 111.72 -4.52 1.70e+00 3.46e-01 7.06e+00 angle pdb=" C LEU C 496 " pdb=" N ASN C 497 " pdb=" CA ASN C 497 " ideal model delta sigma weight residual 121.14 116.67 4.47 1.75e+00 3.27e-01 6.52e+00 ... (remaining 28992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 11509 17.63 - 35.26: 1152 35.26 - 52.88: 312 52.88 - 70.51: 83 70.51 - 88.14: 29 Dihedral angle restraints: 13085 sinusoidal: 5613 harmonic: 7472 Sorted by residual: dihedral pdb=" CG ARG A1131 " pdb=" CD ARG A1131 " pdb=" NE ARG A1131 " pdb=" CZ ARG A1131 " ideal model delta sinusoidal sigma weight residual 180.00 135.06 44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A2212 " pdb=" CD ARG A2212 " pdb=" NE ARG A2212 " pdb=" CZ ARG A2212 " ideal model delta sinusoidal sigma weight residual 90.00 134.89 -44.89 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA LEU A1675 " pdb=" C LEU A1675 " pdb=" N TYR A1676 " pdb=" CA TYR A1676 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 13082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2312 0.036 - 0.072: 748 0.072 - 0.108: 203 0.108 - 0.144: 50 0.144 - 0.180: 1 Chirality restraints: 3314 Sorted by residual: chirality pdb=" CB ILE A1521 " pdb=" CA ILE A1521 " pdb=" CG1 ILE A1521 " pdb=" CG2 ILE A1521 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA VAL A 920 " pdb=" N VAL A 920 " pdb=" C VAL A 920 " pdb=" CB VAL A 920 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CB THR E 562 " pdb=" CA THR E 562 " pdb=" OG1 THR E 562 " pdb=" CG2 THR E 562 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 3311 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 578 " -0.030 2.00e-02 2.50e+03 5.89e-02 3.46e+01 pdb=" C ILE C 578 " 0.102 2.00e-02 2.50e+03 pdb=" O ILE C 578 " -0.038 2.00e-02 2.50e+03 pdb=" N PRO C 579 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1521 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ILE A1521 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE A1521 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A1522 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 578 " 0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO C 579 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 579 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 579 " 0.045 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 64 2.47 - 3.08: 14096 3.08 - 3.69: 32120 3.69 - 4.29: 49004 4.29 - 4.90: 80976 Nonbonded interactions: 176260 Sorted by model distance: nonbonded pdb=" OD1 ASN E 522 " pdb=" OG SER B 523 " model vdw 1.865 3.040 nonbonded pdb=" O2' U G 7 " pdb=" NH2 ARG A1006 " model vdw 1.900 3.120 nonbonded pdb=" NH2 ARG A 305 " pdb=" OD2 ASP B 706 " model vdw 1.988 3.120 nonbonded pdb=" OD2 ASP A 722 " pdb="MG MG A2304 " model vdw 1.999 2.170 nonbonded pdb=" OD2 ASP A 832 " pdb="MG MG A2304 " model vdw 2.022 2.170 ... (remaining 176255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 479 through 579) selection = (chain 'E' and resid 479 through 579) } 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: 10.080 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.040 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.002 0.035 21386 Z= 0.115 Angle : 0.473 10.902 28998 Z= 0.253 Chirality : 0.039 0.180 3314 Planarity : 0.004 0.084 3608 Dihedral : 15.976 88.141 8229 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.48 % Favored : 98.41 % Rotamer: Outliers : 0.95 % Allowed : 15.05 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.17), residues: 2508 helix: 2.30 (0.14), residues: 1436 sheet: 0.06 (0.41), residues: 165 loop : -0.14 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 532 TYR 0.015 0.001 TYR A1979 PHE 0.018 0.001 PHE A 399 TRP 0.011 0.001 TRP A2234 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (21379) covalent geometry : angle 0.47273 / 0.25 (28997) hydrogen bonds : bond 0.16065 / 11.11 ( 1170) hydrogen bonds : angle 5.30050 / 3.93 ( 3363) metal coordination : bond 0.00315 / 0.16 ( 7) metal coordination : angle 1.31297 / 0.69 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 369 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.5220 (mmm) cc_final: 0.4973 (mmt) REVERT: C 541 LYS cc_start: 0.8250 (mmmt) cc_final: 0.8026 (pttt) REVERT: D 484 PHE cc_start: 0.7008 (m-80) cc_final: 0.6518 (m-80) REVERT: D 555 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8127 (mtm-85) REVERT: A 520 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8388 (mmt) REVERT: A 1078 ARG cc_start: 0.6992 (tpp-160) cc_final: 0.6622 (ttm110) REVERT: A 1203 MET cc_start: 0.8733 (mmm) cc_final: 0.8473 (mmm) REVERT: A 1327 ASN cc_start: 0.8592 (t0) cc_final: 0.8331 (t0) REVERT: A 1482 ASP cc_start: 0.8144 (p0) cc_final: 0.7886 (p0) REVERT: A 1941 MET cc_start: 0.7659 (ttp) cc_final: 0.7333 (ttp) REVERT: A 2025 THR cc_start: 0.6964 (p) cc_final: 0.6734 (t) REVERT: A 2131 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 2215 LYS cc_start: 0.8317 (mtmt) cc_final: 0.8095 (mtmt) outliers start: 22 outliers final: 7 residues processed: 382 average time/residue: 0.6384 time to fit residues: 276.4995 Evaluate side-chains 310 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 301 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2175 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 499 HIS C 539 GLN D 591 ASN A 79 ASN A 313 HIS A 830 GLN A 845 ASN A1066 GLN A1324 GLN A1438 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085408 restraints weight = 37659.390| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.73 r_work: 0.3102 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21386 Z= 0.126 Angle : 0.514 8.208 28998 Z= 0.275 Chirality : 0.041 0.167 3314 Planarity : 0.004 0.049 3608 Dihedral : 8.005 74.297 3106 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.36 % Favored : 98.52 % Rotamer: Outliers : 2.72 % Allowed : 15.09 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.17), residues: 2508 helix: 2.37 (0.14), residues: 1447 sheet: 0.25 (0.42), residues: 166 loop : -0.08 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 495 TYR 0.016 0.001 TYR A 88 PHE 0.020 0.001 PHE A 399 TRP 0.010 0.001 TRP A2222 HIS 0.014 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (21379) covalent geometry : angle 0.51441 / 0.27 (28997) hydrogen bonds : bond 0.04838 / 3.31 ( 1170) hydrogen bonds : angle 4.26726 / 3.18 ( 3363) metal coordination : bond 0.00408 / 0.24 ( 7) metal coordination : angle 0.65256 / 0.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 325 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.6859 (mmm) cc_final: 0.6627 (mmt) REVERT: D 484 PHE cc_start: 0.7760 (m-80) cc_final: 0.7549 (m-80) REVERT: D 532 ARG cc_start: 0.7719 (mmm160) cc_final: 0.7378 (mtt180) REVERT: A 588 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: A 755 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8630 (ttm) REVERT: A 1032 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7136 (mmp) REVERT: A 1064 ASP cc_start: 0.6968 (t0) cc_final: 0.6544 (t0) REVERT: A 1078 ARG cc_start: 0.6799 (tpp-160) cc_final: 0.6486 (ttm110) REVERT: A 1327 ASN cc_start: 0.8766 (t0) cc_final: 0.8519 (t0) REVERT: A 1438 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7108 (tm130) REVERT: A 2131 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7794 (t80) REVERT: A 2215 LYS cc_start: 0.8297 (mtmt) cc_final: 0.8022 (ptpt) REVERT: B 658 ASP cc_start: 0.7080 (p0) cc_final: 0.6806 (p0) outliers start: 63 outliers final: 18 residues processed: 358 average time/residue: 0.6648 time to fit residues: 268.5635 Evaluate side-chains 323 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 301 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain E residue 515 SER Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain B residue 650 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 151 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 251 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 497 ASN C 548 ASN D 591 ASN A 79 ASN A 213 ASN A 548 GLN A 845 ASN A1066 GLN A1179 ASN A1324 GLN A1616 HIS A1617 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079178 restraints weight = 37237.623| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.72 r_work: 0.2977 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21386 Z= 0.177 Angle : 0.557 7.591 28998 Z= 0.294 Chirality : 0.043 0.172 3314 Planarity : 0.004 0.043 3608 Dihedral : 7.995 74.402 3091 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.59 % Favored : 98.33 % Rotamer: Outliers : 3.15 % Allowed : 15.35 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.17), residues: 2508 helix: 2.37 (0.14), residues: 1435 sheet: 0.38 (0.43), residues: 159 loop : -0.15 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 661 TYR 0.018 0.002 TYR A 88 PHE 0.023 0.002 PHE A 399 TRP 0.014 0.001 TRP A2234 HIS 0.011 0.001 HIS D 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (21379) covalent geometry : angle 0.55741 / 0.29 (28997) hydrogen bonds : bond 0.05209 / 3.54 ( 1170) hydrogen bonds : angle 4.14215 / 3.08 ( 3363) metal coordination : bond 0.00528 / 0.31 ( 7) metal coordination : angle 1.04129 / 0.55 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: C 497 ASN cc_start: 0.8281 (m-40) cc_final: 0.7813 (m110) REVERT: C 518 MET cc_start: 0.7317 (mmm) cc_final: 0.7058 (mmp) REVERT: C 531 MET cc_start: 0.8351 (tpp) cc_final: 0.8011 (mmp) REVERT: D 532 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7525 (mtt180) REVERT: A 501 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: A 588 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: A 755 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8706 (ttm) REVERT: A 1041 MET cc_start: 0.9089 (mmm) cc_final: 0.8860 (mmm) REVERT: A 1064 ASP cc_start: 0.7242 (t0) cc_final: 0.6632 (t0) REVERT: A 1078 ARG cc_start: 0.6869 (tpp-160) cc_final: 0.6495 (ttm110) REVERT: A 1133 GLU cc_start: 0.7832 (tp30) cc_final: 0.7567 (mm-30) REVERT: A 1438 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7312 (tm130) REVERT: A 1564 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8077 (mpt180) REVERT: A 2024 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7426 (ptpp) REVERT: A 2105 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: A 2131 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 2176 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7816 (mtmt) REVERT: B 692 GLU cc_start: 0.6871 (tp30) cc_final: 0.6615 (tm-30) REVERT: B 695 GLN cc_start: 0.7545 (tp40) cc_final: 0.6813 (mt0) outliers start: 73 outliers final: 28 residues processed: 348 average time/residue: 0.6510 time to fit residues: 254.8254 Evaluate side-chains 328 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2176 LYS Chi-restraints excluded: chain A residue 2191 VAL Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 167 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 147 optimal weight: 0.0970 chunk 190 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 454 GLN A 845 ASN A1324 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079326 restraints weight = 37295.888| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.73 r_work: 0.2980 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21386 Z= 0.136 Angle : 0.503 7.070 28998 Z= 0.266 Chirality : 0.041 0.157 3314 Planarity : 0.004 0.044 3608 Dihedral : 7.919 74.269 3091 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.44 % Favored : 98.48 % Rotamer: Outliers : 2.67 % Allowed : 16.52 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2508 helix: 2.50 (0.14), residues: 1433 sheet: 0.42 (0.43), residues: 159 loop : -0.17 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.014 0.001 TYR A 470 PHE 0.021 0.001 PHE A 399 TRP 0.012 0.001 TRP A2234 HIS 0.010 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (21379) covalent geometry : angle 0.50260 / 0.27 (28997) hydrogen bonds : bond 0.04594 / 3.14 ( 1170) hydrogen bonds : angle 3.98947 / 2.98 ( 3363) metal coordination : bond 0.00399 / 0.24 ( 7) metal coordination : angle 0.57267 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.7414 (mmm) cc_final: 0.7154 (mmp) REVERT: D 532 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7599 (mtt180) REVERT: D 589 LYS cc_start: 0.7836 (tttm) cc_final: 0.7574 (tmtm) REVERT: A 202 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8285 (ttm-80) REVERT: A 430 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8227 (mpt-90) REVERT: A 501 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: A 588 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: A 755 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8686 (ttm) REVERT: A 1064 ASP cc_start: 0.7233 (t0) cc_final: 0.6631 (t0) REVERT: A 1078 ARG cc_start: 0.6871 (tpp-160) cc_final: 0.6521 (ttm110) REVERT: A 1438 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7377 (tm130) REVERT: A 1564 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7936 (mpt180) REVERT: A 2024 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7427 (ptpp) REVERT: A 2105 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 2131 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7830 (t80) REVERT: A 2176 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7800 (mtmt) REVERT: B 695 GLN cc_start: 0.7618 (tp40) cc_final: 0.7044 (mt0) outliers start: 62 outliers final: 25 residues processed: 338 average time/residue: 0.6266 time to fit residues: 238.5990 Evaluate side-chains 320 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2176 LYS Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 70 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 845 ASN A1324 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.077448 restraints weight = 37189.937| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.72 r_work: 0.2943 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21386 Z= 0.178 Angle : 0.533 8.173 28998 Z= 0.283 Chirality : 0.043 0.174 3314 Planarity : 0.004 0.045 3608 Dihedral : 7.988 74.379 3091 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.63 % Favored : 98.29 % Rotamer: Outliers : 3.41 % Allowed : 16.52 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.17), residues: 2508 helix: 2.40 (0.14), residues: 1435 sheet: 0.38 (0.42), residues: 159 loop : -0.23 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1180 TYR 0.018 0.002 TYR E 498 PHE 0.024 0.002 PHE A 399 TRP 0.013 0.001 TRP A2234 HIS 0.022 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (21379) covalent geometry : angle 0.53297 / 0.28 (28997) hydrogen bonds : bond 0.04945 / 3.37 ( 1170) hydrogen bonds : angle 4.04632 / 3.01 ( 3363) metal coordination : bond 0.00622 / 0.39 ( 7) metal coordination : angle 0.82741 / 0.44 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 296 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.7666 (mmm) cc_final: 0.7347 (mmp) REVERT: D 518 MET cc_start: 0.7183 (mtm) cc_final: 0.6968 (mmm) REVERT: D 532 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7611 (mtt180) REVERT: D 589 LYS cc_start: 0.7867 (tttm) cc_final: 0.7578 (tmtm) REVERT: A 202 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8318 (ttm-80) REVERT: A 204 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8212 (tmtp) REVERT: A 330 ASP cc_start: 0.7989 (t0) cc_final: 0.7669 (t70) REVERT: A 375 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: A 430 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8241 (mpt-90) REVERT: A 501 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 513 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: A 588 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: A 755 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8715 (ttm) REVERT: A 824 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7365 (mmm160) REVERT: A 1032 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7625 (mtp) REVERT: A 1064 ASP cc_start: 0.7293 (t0) cc_final: 0.6662 (t0) REVERT: A 1078 ARG cc_start: 0.6868 (tpp-160) cc_final: 0.6461 (ttm110) REVERT: A 1133 GLU cc_start: 0.7870 (tp30) cc_final: 0.7606 (mm-30) REVERT: A 1438 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7400 (tm130) REVERT: A 2024 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7413 (ptpp) REVERT: A 2105 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: A 2131 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7664 (t80) REVERT: A 2176 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7828 (mtmt) REVERT: A 2215 LYS cc_start: 0.8342 (mtmt) cc_final: 0.8117 (mtmt) REVERT: B 695 GLN cc_start: 0.7740 (tp40) cc_final: 0.7320 (mt0) outliers start: 79 outliers final: 35 residues processed: 342 average time/residue: 0.6736 time to fit residues: 259.4079 Evaluate side-chains 329 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 281 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2176 LYS Chi-restraints excluded: chain A residue 2191 VAL Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 239 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.0470 chunk 192 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 845 ASN A1324 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078449 restraints weight = 36950.041| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.74 r_work: 0.2964 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21386 Z= 0.124 Angle : 0.488 8.279 28998 Z= 0.258 Chirality : 0.040 0.155 3314 Planarity : 0.004 0.045 3608 Dihedral : 7.875 74.276 3091 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.36 % Favored : 98.56 % Rotamer: Outliers : 2.50 % Allowed : 18.11 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.17), residues: 2508 helix: 2.55 (0.14), residues: 1435 sheet: 0.44 (0.42), residues: 159 loop : -0.22 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 495 TYR 0.015 0.001 TYR A 470 PHE 0.020 0.001 PHE A 399 TRP 0.013 0.001 TRP A1248 HIS 0.007 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21379) covalent geometry : angle 0.48798 / 0.26 (28997) hydrogen bonds : bond 0.04389 / 3.01 ( 1170) hydrogen bonds : angle 3.90150 / 2.91 ( 3363) metal coordination : bond 0.00375 / 0.23 ( 7) metal coordination : angle 0.14163 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.7649 (mmm) cc_final: 0.7326 (mmp) REVERT: D 518 MET cc_start: 0.7121 (mtm) cc_final: 0.6911 (mmm) REVERT: D 589 LYS cc_start: 0.7850 (tttm) cc_final: 0.7563 (tmtm) REVERT: A 202 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8320 (ttm-80) REVERT: A 204 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8160 (tmtp) REVERT: A 330 ASP cc_start: 0.7972 (t0) cc_final: 0.7658 (t70) REVERT: A 375 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: A 588 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: A 755 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8693 (ttm) REVERT: A 824 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7296 (mmm160) REVERT: A 1032 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7667 (mtp) REVERT: A 1064 ASP cc_start: 0.7302 (t0) cc_final: 0.6830 (t0) REVERT: A 1078 ARG cc_start: 0.6785 (tpp-160) cc_final: 0.6431 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7764 (tp30) cc_final: 0.7494 (mm-30) REVERT: A 1438 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7299 (tm130) REVERT: A 1442 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: A 2024 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7376 (ptpp) REVERT: A 2105 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: A 2131 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7827 (t80) REVERT: A 2176 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: B 695 GLN cc_start: 0.7713 (tp40) cc_final: 0.7443 (mt0) outliers start: 58 outliers final: 24 residues processed: 323 average time/residue: 0.7107 time to fit residues: 258.3886 Evaluate side-chains 318 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2176 LYS Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain A residue 2224 VAL Chi-restraints excluded: chain B residue 496 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 185 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 169 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 845 ASN A1324 GLN A2045 GLN B 502 HIS B 561 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.095944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078591 restraints weight = 37033.626| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.72 r_work: 0.2967 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21386 Z= 0.118 Angle : 0.487 8.798 28998 Z= 0.256 Chirality : 0.040 0.153 3314 Planarity : 0.004 0.045 3608 Dihedral : 7.834 74.260 3091 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.40 % Favored : 98.52 % Rotamer: Outliers : 2.89 % Allowed : 17.98 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.17), residues: 2508 helix: 2.58 (0.14), residues: 1438 sheet: 0.24 (0.42), residues: 166 loop : -0.16 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 555 TYR 0.017 0.001 TYR E 498 PHE 0.020 0.001 PHE A 399 TRP 0.012 0.001 TRP A2234 HIS 0.008 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21379) covalent geometry : angle 0.48663 / 0.26 (28997) hydrogen bonds : bond 0.04270 / 2.92 ( 1170) hydrogen bonds : angle 3.86804 / 2.89 ( 3363) metal coordination : bond 0.00326 / 0.20 ( 7) metal coordination : angle 0.21214 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.7676 (mmm) cc_final: 0.7340 (mmp) REVERT: D 589 LYS cc_start: 0.7848 (tttm) cc_final: 0.7564 (tmtm) REVERT: A 202 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8324 (ttm-80) REVERT: A 204 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8141 (tmtp) REVERT: A 330 ASP cc_start: 0.7976 (t0) cc_final: 0.7673 (t70) REVERT: A 375 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: A 501 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: A 513 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: A 588 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: A 755 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8682 (ttm) REVERT: A 824 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7286 (mmm160) REVERT: A 972 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7467 (p) REVERT: A 1032 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7655 (mtp) REVERT: A 1064 ASP cc_start: 0.7295 (t0) cc_final: 0.6662 (t0) REVERT: A 1078 ARG cc_start: 0.6787 (tpp-160) cc_final: 0.6459 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7758 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 1438 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7378 (tm130) REVERT: A 1442 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: A 2024 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7370 (ptpp) REVERT: A 2105 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: A 2131 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7871 (t80) REVERT: A 2215 LYS cc_start: 0.8265 (mtmt) cc_final: 0.8064 (mtmt) REVERT: B 521 ILE cc_start: 0.8313 (mm) cc_final: 0.8081 (mm) REVERT: B 695 GLN cc_start: 0.7712 (tp40) cc_final: 0.7480 (mt0) outliers start: 67 outliers final: 30 residues processed: 330 average time/residue: 0.6842 time to fit residues: 254.8126 Evaluate side-chains 326 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain A residue 2224 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 689 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 39 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 845 ASN A1174 ASN A1324 GLN A2045 GLN B 502 HIS B 561 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077811 restraints weight = 36949.310| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.72 r_work: 0.2951 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21386 Z= 0.150 Angle : 0.509 9.094 28998 Z= 0.267 Chirality : 0.041 0.155 3314 Planarity : 0.004 0.046 3608 Dihedral : 7.864 74.271 3091 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.36 % Favored : 98.56 % Rotamer: Outliers : 3.10 % Allowed : 17.90 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.17), residues: 2508 helix: 2.54 (0.14), residues: 1438 sheet: 0.47 (0.41), residues: 171 loop : -0.23 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 555 TYR 0.015 0.001 TYR A 470 PHE 0.022 0.001 PHE A 399 TRP 0.012 0.001 TRP A2234 HIS 0.007 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (21379) covalent geometry : angle 0.50919 / 0.27 (28997) hydrogen bonds : bond 0.04500 / 3.08 ( 1170) hydrogen bonds : angle 3.90839 / 2.91 ( 3363) metal coordination : bond 0.00468 / 0.29 ( 7) metal coordination : angle 0.76860 / 0.40 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.7764 (mmm) cc_final: 0.7421 (mmp) REVERT: D 589 LYS cc_start: 0.7852 (tttm) cc_final: 0.7569 (tmtm) REVERT: A 202 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8354 (ttm-80) REVERT: A 204 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8125 (tmtp) REVERT: A 330 ASP cc_start: 0.7988 (t0) cc_final: 0.7694 (t70) REVERT: A 375 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: A 501 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: A 513 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: A 588 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: A 755 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8703 (ttm) REVERT: A 824 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7324 (mmm160) REVERT: A 972 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7479 (p) REVERT: A 1032 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7649 (mtp) REVERT: A 1064 ASP cc_start: 0.7331 (t0) cc_final: 0.6822 (t0) REVERT: A 1078 ARG cc_start: 0.6861 (tpp-160) cc_final: 0.6483 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7782 (tp30) cc_final: 0.7511 (mm-30) REVERT: A 1438 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7395 (tm130) REVERT: A 1442 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: A 2024 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7378 (ptpp) REVERT: A 2105 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: A 2131 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7808 (t80) REVERT: B 521 ILE cc_start: 0.8431 (mm) cc_final: 0.8182 (mm) REVERT: B 682 ILE cc_start: 0.8163 (mm) cc_final: 0.7924 (mp) REVERT: B 695 GLN cc_start: 0.7723 (tp40) cc_final: 0.7512 (mt0) outliers start: 72 outliers final: 37 residues processed: 330 average time/residue: 0.6422 time to fit residues: 238.8983 Evaluate side-chains 334 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 1980 THR Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain A residue 2224 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 179 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 845 ASN A1324 GLN A2045 GLN B 497 ASN B 502 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.077676 restraints weight = 36839.112| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.71 r_work: 0.2951 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21386 Z= 0.145 Angle : 0.514 11.854 28998 Z= 0.270 Chirality : 0.041 0.156 3314 Planarity : 0.004 0.046 3608 Dihedral : 7.869 74.316 3091 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.20 % Favored : 98.72 % Rotamer: Outliers : 2.76 % Allowed : 18.41 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.17), residues: 2508 helix: 2.52 (0.14), residues: 1438 sheet: 0.48 (0.42), residues: 159 loop : -0.23 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1180 TYR 0.024 0.001 TYR E 498 PHE 0.022 0.001 PHE A 399 TRP 0.012 0.001 TRP A2234 HIS 0.006 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (21379) covalent geometry : angle 0.51385 / 0.27 (28997) hydrogen bonds : bond 0.04526 / 3.09 ( 1170) hydrogen bonds : angle 3.91259 / 2.91 ( 3363) metal coordination : bond 0.00485 / 0.31 ( 7) metal coordination : angle 0.50828 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 290 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 589 LYS cc_start: 0.7848 (tttm) cc_final: 0.7570 (tmtm) REVERT: A 202 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8325 (ttm-80) REVERT: A 204 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8155 (tmtp) REVERT: A 330 ASP cc_start: 0.8000 (t0) cc_final: 0.7704 (t70) REVERT: A 375 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: A 501 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: A 513 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: A 588 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: A 755 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8714 (ttm) REVERT: A 824 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7320 (mmm160) REVERT: A 972 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7492 (p) REVERT: A 1032 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7683 (mtp) REVERT: A 1064 ASP cc_start: 0.7353 (t0) cc_final: 0.6840 (t0) REVERT: A 1078 ARG cc_start: 0.6879 (tpp-160) cc_final: 0.6587 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7756 (tp30) cc_final: 0.7479 (mm-30) REVERT: A 1438 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7392 (tm130) REVERT: A 1442 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: A 2024 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7336 (ptpp) REVERT: A 2105 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: A 2131 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 521 ILE cc_start: 0.8556 (mm) cc_final: 0.8258 (mt) REVERT: B 682 ILE cc_start: 0.8240 (mm) cc_final: 0.8020 (mp) outliers start: 64 outliers final: 40 residues processed: 330 average time/residue: 0.6980 time to fit residues: 259.2615 Evaluate side-chains 337 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1980 THR Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2191 VAL Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain A residue 2224 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.0980 chunk 186 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 845 ASN A1324 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077765 restraints weight = 37205.355| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.71 r_work: 0.2951 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21386 Z= 0.137 Angle : 0.523 12.804 28998 Z= 0.272 Chirality : 0.041 0.155 3314 Planarity : 0.004 0.046 3608 Dihedral : 7.858 74.309 3091 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.24 % Favored : 98.68 % Rotamer: Outliers : 2.63 % Allowed : 18.63 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.17), residues: 2508 helix: 2.53 (0.14), residues: 1440 sheet: 0.50 (0.41), residues: 171 loop : -0.23 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.015 0.001 TYR A 470 PHE 0.021 0.001 PHE A 399 TRP 0.012 0.001 TRP A2234 HIS 0.007 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21379) covalent geometry : angle 0.52297 / 0.27 (28997) hydrogen bonds : bond 0.04466 / 3.05 ( 1170) hydrogen bonds : angle 3.90749 / 2.92 ( 3363) metal coordination : bond 0.00418 / 0.26 ( 7) metal coordination : angle 0.57300 / 0.30 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: D 589 LYS cc_start: 0.7830 (tttm) cc_final: 0.7555 (tmtm) REVERT: A 202 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8316 (ttm-80) REVERT: A 204 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8178 (tmtp) REVERT: A 330 ASP cc_start: 0.7991 (t0) cc_final: 0.7712 (t70) REVERT: A 375 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: A 501 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: A 513 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 588 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: A 755 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8705 (ttm) REVERT: A 824 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7293 (mmm160) REVERT: A 972 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7486 (p) REVERT: A 1032 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7675 (mtp) REVERT: A 1064 ASP cc_start: 0.7353 (t0) cc_final: 0.6830 (t0) REVERT: A 1078 ARG cc_start: 0.6929 (tpp-160) cc_final: 0.6597 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7741 (tp30) cc_final: 0.7460 (mm-30) REVERT: A 1438 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7380 (tm130) REVERT: A 1442 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: A 2024 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7318 (ptpp) REVERT: A 2067 LYS cc_start: 0.8888 (tptm) cc_final: 0.8654 (ttpp) REVERT: A 2105 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 2131 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 2215 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8190 (mtmt) REVERT: B 521 ILE cc_start: 0.8606 (mm) cc_final: 0.8327 (mt) REVERT: B 676 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7530 (mt-10) REVERT: B 682 ILE cc_start: 0.8262 (mm) cc_final: 0.8051 (mp) outliers start: 61 outliers final: 39 residues processed: 328 average time/residue: 0.7097 time to fit residues: 262.2723 Evaluate side-chains 338 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 593 GLU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 1868 ILE Chi-restraints excluded: chain A residue 1980 THR Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2072 ILE Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2131 TYR Chi-restraints excluded: chain A residue 2191 VAL Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain A residue 2224 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 689 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 44 optimal weight: 0.0970 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 845 ASN A1324 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077322 restraints weight = 37109.705| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.72 r_work: 0.2943 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21386 Z= 0.153 Angle : 0.533 12.378 28998 Z= 0.277 Chirality : 0.042 0.329 3314 Planarity : 0.004 0.046 3608 Dihedral : 7.882 74.366 3091 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.28 % Favored : 98.64 % Rotamer: Outliers : 2.63 % Allowed : 18.59 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2508 helix: 2.52 (0.14), residues: 1432 sheet: 0.48 (0.42), residues: 159 loop : -0.24 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1180 TYR 0.026 0.002 TYR E 498 PHE 0.022 0.001 PHE A 399 TRP 0.012 0.001 TRP A2234 HIS 0.007 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (21379) covalent geometry : angle 0.53280 / 0.28 (28997) hydrogen bonds : bond 0.04606 / 3.15 ( 1170) hydrogen bonds : angle 3.94869 / 2.94 ( 3363) metal coordination : bond 0.00549 / 0.35 ( 7) metal coordination : angle 0.97620 / 0.51 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7662.70 seconds wall clock time: 131 minutes 26.73 seconds (7886.73 seconds total)