Starting phenix.real_space_refine on Wed May 21 07:40:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gju_51403/05_2025/9gju_51403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gju_51403/05_2025/9gju_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_51403/05_2025/9gju_51403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gju_51403/05_2025/9gju_51403.map" model { file = "/net/cci-nas-00/data/ceres_data/9gju_51403/05_2025/9gju_51403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gju_51403/05_2025/9gju_51403.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.18, per 1000 atoms: 0.58 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: 5.34 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.51 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: 7.92 Time building geometry restraints manager: 6.22 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: 4.400 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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= 0.113 Angle : 0.473 10.902 28998 Z= 0.251 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.001 TRP A2234 HIS 0.005 0.001 HIS B 499 PHE 0.018 0.001 PHE A 399 TYR 0.015 0.001 TYR A1979 ARG 0.003 0.000 ARG E 532 Details of bonding type rmsd hydrogen bonds : bond 0.16065 ( 1170) hydrogen bonds : angle 5.30050 ( 3363) metal coordination : bond 0.00315 ( 7) metal coordination : angle 1.31297 ( 1) covalent geometry : bond 0.00235 (21379) covalent geometry : angle 0.47272 (28997) *********************** 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 : 2.519 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: 1.3659 time to fit residues: 591.7486 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 : 2.470 ------------------------------------------------------------------------------- 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 213 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 198 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 147 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 539 GLN D 591 ASN A 79 ASN A 313 HIS A 830 GLN A 845 ASN A1066 GLN A1324 GLN A1438 GLN A1965 ASN 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 = 0.3496 r_free = 0.3496 target = 0.100931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083203 restraints weight = 37262.397| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.73 r_work: 0.3053 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21386 Z= 0.136 Angle : 0.516 8.349 28998 Z= 0.275 Chirality : 0.041 0.173 3314 Planarity : 0.004 0.045 3608 Dihedral : 8.029 74.362 3106 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.44 % Favored : 98.44 % Rotamer: Outliers : 3.10 % Allowed : 14.83 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.17), residues: 2508 helix: 2.38 (0.14), residues: 1436 sheet: 0.50 (0.43), residues: 156 loop : -0.08 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1248 HIS 0.013 0.001 HIS B 502 PHE 0.022 0.001 PHE A 399 TYR 0.017 0.001 TYR A 88 ARG 0.006 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 1170) hydrogen bonds : angle 4.17937 ( 3363) metal coordination : bond 0.00246 ( 7) metal coordination : angle 1.24965 ( 1) covalent geometry : bond 0.00297 (21379) covalent geometry : angle 0.51628 (28997) *********************** 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 395 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 2.354 Fit side-chains revert: symmetry clash REVERT: C 518 MET cc_start: 0.6936 (mmm) cc_final: 0.6682 (mmt) REVERT: D 532 ARG cc_start: 0.7695 (mmm160) cc_final: 0.7416 (mtt180) REVERT: D 591 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7768 (t0) REVERT: A 375 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: A 588 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: A 755 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8643 (ttm) REVERT: A 824 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7209 (mmm160) REVERT: A 1032 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7182 (mmp) REVERT: A 1064 ASP cc_start: 0.7106 (t0) cc_final: 0.6598 (t0) REVERT: A 1078 ARG cc_start: 0.6669 (tpp-160) cc_final: 0.6380 (ttm110) REVERT: A 1633 MET cc_start: 0.8659 (ttp) cc_final: 0.8373 (ttp) REVERT: A 2131 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 662 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7328 (t70) REVERT: B 692 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6284 (tm-30) outliers start: 72 outliers final: 18 residues processed: 359 average time/residue: 1.4329 time to fit residues: 580.6031 Evaluate side-chains 323 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 591 ASN Chi-restraints excluded: chain E residue 515 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 336 MET 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 810 THR 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 1051 LEU Chi-restraints excluded: chain A residue 1071 THR 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 1695 CYS 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 Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 692 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 204 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 86 optimal weight: 0.0020 chunk 202 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 497 ASN C 548 ASN D 591 ASN A 79 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN A1066 GLN A1179 ASN A1324 GLN A1438 GLN A1617 GLN A1965 ASN A2045 GLN B 502 HIS B 708 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.080984 restraints weight = 36991.507| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.72 r_work: 0.3014 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21386 Z= 0.129 Angle : 0.497 8.261 28998 Z= 0.262 Chirality : 0.041 0.159 3314 Planarity : 0.004 0.044 3608 Dihedral : 7.852 74.263 3091 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.48 % Favored : 98.44 % Rotamer: Outliers : 3.15 % Allowed : 15.78 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2508 helix: 2.52 (0.14), residues: 1430 sheet: 0.27 (0.42), residues: 166 loop : -0.00 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2234 HIS 0.011 0.001 HIS B 502 PHE 0.021 0.001 PHE A 399 TYR 0.014 0.001 TYR A 88 ARG 0.004 0.000 ARG C 495 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 1170) hydrogen bonds : angle 4.00029 ( 3363) metal coordination : bond 0.00359 ( 7) metal coordination : angle 0.04377 ( 1) covalent geometry : bond 0.00290 (21379) covalent geometry : angle 0.49706 (28997) *********************** 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 379 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 306 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 497 ASN cc_start: 0.8230 (m-40) cc_final: 0.7731 (m110) REVERT: C 518 MET cc_start: 0.7194 (mmm) cc_final: 0.6931 (mmt) REVERT: D 532 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7496 (mtt180) REVERT: A 375 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: A 501 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 588 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: A 755 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8646 (ttm) REVERT: A 803 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7856 (tp-100) REVERT: A 824 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7273 (mmm160) REVERT: A 1064 ASP cc_start: 0.7177 (t0) cc_final: 0.6552 (t0) REVERT: A 1096 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7310 (mmmm) REVERT: A 1438 GLN cc_start: 0.7589 (tm130) cc_final: 0.7378 (tm-30) REVERT: A 1564 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7894 (mpt180) REVERT: A 1633 MET cc_start: 0.8653 (ttp) cc_final: 0.8400 (ttp) REVERT: A 2024 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7401 (ptpp) REVERT: A 2105 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 2131 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7868 (t80) REVERT: A 2176 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7772 (mtmt) REVERT: B 689 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: B 695 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6605 (mt0) outliers start: 73 outliers final: 28 residues processed: 346 average time/residue: 1.4866 time to fit residues: 581.7994 Evaluate side-chains 335 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 572 VAL 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 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 803 GLN 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 1051 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1313 GLU 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 114 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 213 ASN A 548 GLN A 845 ASN A1324 GLN A1438 GLN A1616 HIS A2045 GLN B 502 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079318 restraints weight = 37391.795| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.74 r_work: 0.2981 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2395 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= 0.136 Angle : 0.494 7.339 28998 Z= 0.261 Chirality : 0.041 0.159 3314 Planarity : 0.004 0.044 3608 Dihedral : 7.827 74.246 3091 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.44 % Favored : 98.48 % Rotamer: Outliers : 3.19 % Allowed : 16.26 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.17), residues: 2508 helix: 2.57 (0.14), residues: 1433 sheet: 0.56 (0.43), residues: 156 loop : -0.10 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2234 HIS 0.011 0.001 HIS C 499 PHE 0.021 0.001 PHE A 399 TYR 0.018 0.001 TYR E 498 ARG 0.005 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 1170) hydrogen bonds : angle 3.89747 ( 3363) metal coordination : bond 0.00416 ( 7) metal coordination : angle 0.06868 ( 1) covalent geometry : bond 0.00307 (21379) covalent geometry : angle 0.49384 (28997) *********************** 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 381 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 518 MET cc_start: 0.7458 (mmm) cc_final: 0.7161 (mmp) REVERT: D 532 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7532 (mtt180) REVERT: A 202 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8180 (mtp85) REVERT: A 375 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: A 501 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: A 588 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: A 755 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8685 (ttm) REVERT: A 824 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7306 (mmm160) REVERT: A 1064 ASP cc_start: 0.7249 (t0) cc_final: 0.6618 (t0) REVERT: A 1096 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7395 (mmmm) REVERT: A 1133 GLU cc_start: 0.7801 (tp30) cc_final: 0.7537 (mm-30) REVERT: A 1564 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7983 (mpt180) REVERT: A 1633 MET cc_start: 0.8676 (ttp) cc_final: 0.8424 (ttp) REVERT: A 2024 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7360 (ptpp) REVERT: A 2105 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 2131 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 2176 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7808 (mtmt) REVERT: B 695 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6904 (mt0) outliers start: 74 outliers final: 28 residues processed: 347 average time/residue: 1.4575 time to fit residues: 570.2877 Evaluate side-chains 329 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 290 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain D residue 572 VAL 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 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 824 ARG Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1313 GLU 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS 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 565 SER Chi-restraints excluded: chain B residue 689 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 71 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 191 optimal weight: 0.0870 chunk 239 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 ASN A 79 ASN A 845 ASN A1324 GLN A1438 GLN A2045 GLN B 497 ASN B 502 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079098 restraints weight = 37234.234| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.73 r_work: 0.2978 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2597 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= 0.123 Angle : 0.478 7.930 28998 Z= 0.253 Chirality : 0.040 0.159 3314 Planarity : 0.004 0.045 3608 Dihedral : 7.781 74.218 3091 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.48 % Favored : 98.44 % Rotamer: Outliers : 3.10 % Allowed : 17.21 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.17), residues: 2508 helix: 2.61 (0.14), residues: 1435 sheet: 0.32 (0.42), residues: 166 loop : -0.06 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2234 HIS 0.008 0.001 HIS B 502 PHE 0.020 0.001 PHE A 399 TYR 0.013 0.001 TYR A 88 ARG 0.004 0.000 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1170) hydrogen bonds : angle 3.83235 ( 3363) metal coordination : bond 0.00358 ( 7) metal coordination : angle 0.29034 ( 1) covalent geometry : bond 0.00277 (21379) covalent geometry : angle 0.47820 (28997) *********************** 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 370 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 479 MET cc_start: 0.5480 (tpp) cc_final: 0.5227 (ttp) REVERT: C 518 MET cc_start: 0.7542 (mmm) cc_final: 0.7229 (mmp) REVERT: D 532 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7583 (mtt180) REVERT: D 589 LYS cc_start: 0.7811 (tmtt) cc_final: 0.7390 (tmtm) REVERT: E 575 MET cc_start: 0.8496 (mmm) cc_final: 0.8191 (mtp) REVERT: A 202 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8177 (mtp85) REVERT: A 204 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8185 (tmtp) REVERT: A 375 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: A 501 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: A 513 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 580 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8408 (ttpp) REVERT: A 588 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: A 755 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8689 (ttm) REVERT: A 803 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: A 824 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7280 (mmm160) REVERT: A 1032 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7603 (mtp) REVERT: A 1064 ASP cc_start: 0.7248 (t0) cc_final: 0.6615 (t0) REVERT: A 1133 GLU cc_start: 0.7788 (tp30) cc_final: 0.7526 (mm-30) REVERT: A 1438 GLN cc_start: 0.7697 (tm130) cc_final: 0.7426 (tm-30) REVERT: A 1564 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8066 (mpt180) REVERT: A 1633 MET cc_start: 0.8674 (ttp) cc_final: 0.8436 (ttp) REVERT: A 2024 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7364 (ptpp) REVERT: A 2105 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: A 2131 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7854 (t80) REVERT: A 2176 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7803 (mtmt) REVERT: B 695 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7118 (mt0) outliers start: 72 outliers final: 28 residues processed: 336 average time/residue: 1.5422 time to fit residues: 581.7459 Evaluate side-chains 328 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 572 VAL 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 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 803 GLN 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 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 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS 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 2191 VAL Chi-restraints excluded: chain A residue 2221 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 565 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 6 optimal weight: 0.0370 chunk 140 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 ASN A 79 ASN A 845 ASN A1324 GLN A1438 GLN A2045 GLN B 502 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.077321 restraints weight = 36955.770| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.72 r_work: 0.2942 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21386 Z= 0.166 Angle : 0.523 8.976 28998 Z= 0.276 Chirality : 0.042 0.161 3314 Planarity : 0.004 0.046 3608 Dihedral : 7.895 74.297 3091 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.44 % Favored : 98.48 % Rotamer: Outliers : 3.10 % Allowed : 17.55 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2508 helix: 2.51 (0.14), residues: 1430 sheet: 0.52 (0.43), residues: 159 loop : -0.15 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2234 HIS 0.007 0.001 HIS B 502 PHE 0.024 0.002 PHE A 399 TYR 0.018 0.002 TYR E 498 ARG 0.006 0.000 ARG A1131 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 1170) hydrogen bonds : angle 3.93446 ( 3363) metal coordination : bond 0.00494 ( 7) metal coordination : angle 0.93454 ( 1) covalent geometry : bond 0.00393 (21379) covalent geometry : angle 0.52323 (28997) *********************** 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 363 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 291 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: C 479 MET cc_start: 0.5412 (tpp) cc_final: 0.5202 (ttp) REVERT: C 518 MET cc_start: 0.7796 (mmm) cc_final: 0.7460 (mmp) REVERT: D 532 ARG cc_start: 0.7962 (mmm160) cc_final: 0.7676 (mmt180) REVERT: D 589 LYS cc_start: 0.7847 (tmtt) cc_final: 0.7543 (tmtm) REVERT: A 202 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8279 (mtp85) REVERT: A 204 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8187 (tmtp) REVERT: A 375 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: A 501 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 513 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 588 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: A 755 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8744 (ttm) REVERT: A 824 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7340 (mmm160) REVERT: A 1032 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7612 (mtp) REVERT: A 1064 ASP cc_start: 0.7340 (t0) cc_final: 0.6701 (t0) REVERT: A 1078 ARG cc_start: 0.6824 (tpp-160) cc_final: 0.6537 (tmm-80) REVERT: A 1096 LYS cc_start: 0.8019 (tppp) cc_final: 0.7695 (mmmm) REVERT: A 1438 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7442 (tm130) REVERT: A 1442 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: A 1564 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8131 (mpt180) REVERT: A 1633 MET cc_start: 0.8648 (ttp) cc_final: 0.8406 (ttp) REVERT: A 2024 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7385 (ptpp) REVERT: A 2105 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 2131 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 2176 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7850 (mtmt) REVERT: A 2215 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8096 (mtmt) REVERT: B 521 ILE cc_start: 0.8468 (mm) cc_final: 0.8146 (mt) REVERT: B 695 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7291 (mt0) outliers start: 72 outliers final: 34 residues processed: 332 average time/residue: 1.5286 time to fit residues: 570.8687 Evaluate side-chains 335 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 540 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain E residue 515 SER 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 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 868 MET Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 970 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 1386 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2053 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 2110 ILE 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 A residue 2224 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 232 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 845 ASN A1174 ASN A1324 GLN A1965 ASN A2045 GLN B 502 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.076336 restraints weight = 36850.796| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.71 r_work: 0.2925 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21386 Z= 0.190 Angle : 0.546 11.837 28998 Z= 0.287 Chirality : 0.043 0.165 3314 Planarity : 0.004 0.045 3608 Dihedral : 7.989 74.419 3091 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.56 % Favored : 98.37 % Rotamer: Outliers : 3.41 % Allowed : 17.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2508 helix: 2.43 (0.14), residues: 1433 sheet: 0.39 (0.41), residues: 171 loop : -0.28 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2234 HIS 0.008 0.001 HIS B 671 PHE 0.023 0.002 PHE A 399 TYR 0.018 0.002 TYR A1320 ARG 0.004 0.000 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 1170) hydrogen bonds : angle 4.01545 ( 3363) metal coordination : bond 0.00612 ( 7) metal coordination : angle 0.98618 ( 1) covalent geometry : bond 0.00454 (21379) covalent geometry : angle 0.54619 (28997) *********************** 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 377 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 298 time to evaluate : 2.171 Fit side-chains revert: symmetry clash REVERT: D 532 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7832 (mmt180) REVERT: D 589 LYS cc_start: 0.7866 (tmtt) cc_final: 0.7523 (tmtm) REVERT: E 503 LEU cc_start: 0.8455 (mm) cc_final: 0.8192 (mm) REVERT: A 202 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8302 (mtp85) REVERT: A 204 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8225 (tmtp) REVERT: A 375 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: A 501 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 513 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: A 588 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: A 755 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8739 (ttm) REVERT: A 824 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7352 (mmm160) REVERT: A 1032 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7628 (mtp) REVERT: A 1064 ASP cc_start: 0.7406 (t0) cc_final: 0.6850 (t0) REVERT: A 1078 ARG cc_start: 0.6895 (tpp-160) cc_final: 0.6492 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7833 (tp30) cc_final: 0.7574 (mm-30) REVERT: A 1438 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 1442 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 1564 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8295 (mpt180) REVERT: A 2024 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7404 (ptpp) REVERT: A 2105 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 2131 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7691 (t80) REVERT: A 2176 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7858 (mtmt) REVERT: B 521 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 665 LYS cc_start: 0.8848 (tttt) cc_final: 0.8583 (ptmt) REVERT: B 676 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7572 (mt-10) REVERT: B 682 ILE cc_start: 0.8313 (mm) cc_final: 0.8088 (mp) outliers start: 79 outliers final: 40 residues processed: 341 average time/residue: 1.4904 time to fit residues: 572.1166 Evaluate side-chains 345 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 2.320 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 572 VAL 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 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 868 MET Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 970 THR 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 1339 VAL Chi-restraints excluded: chain A residue 1386 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 1868 ILE 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 2080 THR Chi-restraints excluded: chain A residue 2096 LEU 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 A residue 2224 VAL Chi-restraints excluded: chain B residue 521 ILE 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 689 GLU Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 38 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 129 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3394 r_free = 0.3394 target = 0.094731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.077400 restraints weight = 37336.691| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.75 r_work: 0.2946 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21386 Z= 0.131 Angle : 0.507 11.479 28998 Z= 0.266 Chirality : 0.041 0.155 3314 Planarity : 0.004 0.044 3608 Dihedral : 7.873 74.306 3091 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.20 % Favored : 98.72 % Rotamer: Outliers : 2.72 % Allowed : 18.67 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2508 helix: 2.54 (0.14), residues: 1438 sheet: 0.49 (0.41), residues: 171 loop : -0.20 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.006 0.001 HIS B 502 PHE 0.021 0.001 PHE A 399 TYR 0.020 0.001 TYR E 498 ARG 0.004 0.000 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 1170) hydrogen bonds : angle 3.89211 ( 3363) metal coordination : bond 0.00341 ( 7) metal coordination : angle 0.12643 ( 1) covalent geometry : bond 0.00298 (21379) covalent geometry : angle 0.50710 (28997) *********************** 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 359 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 296 time to evaluate : 2.455 Fit side-chains revert: symmetry clash REVERT: D 479 MET cc_start: 0.8437 (mmm) cc_final: 0.7997 (mtm) REVERT: D 532 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7793 (mmt180) REVERT: D 589 LYS cc_start: 0.7839 (tmtt) cc_final: 0.7616 (tmtm) REVERT: E 503 LEU cc_start: 0.8417 (mm) cc_final: 0.8149 (mm) REVERT: A 202 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8266 (mtp85) REVERT: A 204 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8240 (mptt) REVERT: A 375 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: A 501 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 513 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: A 580 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8424 (ttpp) REVERT: A 588 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: A 755 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8700 (ttm) REVERT: A 824 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7319 (mmm160) REVERT: A 1032 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: A 1064 ASP cc_start: 0.7392 (t0) cc_final: 0.6831 (t0) REVERT: A 1078 ARG cc_start: 0.6901 (tpp-160) cc_final: 0.6535 (tmm-80) REVERT: A 1096 LYS cc_start: 0.8026 (tppp) cc_final: 0.7762 (mmmm) REVERT: A 1133 GLU cc_start: 0.7850 (tp30) cc_final: 0.7583 (mm-30) REVERT: A 1438 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7507 (tm-30) REVERT: A 1442 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: A 1564 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8150 (mpt180) REVERT: A 2024 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7359 (ptpp) REVERT: A 2105 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 2115 ASN cc_start: 0.8963 (m-40) cc_final: 0.8583 (m-40) REVERT: A 2131 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7856 (t80) REVERT: A 2215 LYS cc_start: 0.8357 (mtmt) cc_final: 0.8140 (mtmt) REVERT: B 521 ILE cc_start: 0.8676 (mm) cc_final: 0.8426 (mt) REVERT: B 665 LYS cc_start: 0.8865 (tttt) cc_final: 0.8571 (ptmt) REVERT: B 676 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7491 (mt-10) REVERT: B 682 ILE cc_start: 0.8312 (mm) cc_final: 0.8081 (mp) outliers start: 63 outliers final: 37 residues processed: 333 average time/residue: 1.4799 time to fit residues: 556.4628 Evaluate side-chains 343 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 540 VAL Chi-restraints excluded: chain D residue 572 VAL 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 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 868 MET Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 970 THR 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 1339 VAL Chi-restraints excluded: chain A residue 1386 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2053 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 533 LEU Chi-restraints excluded: chain B residue 565 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 136 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 237 optimal weight: 0.5980 chunk 206 optimal weight: 0.0870 chunk 247 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3401 r_free = 0.3401 target = 0.095067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077864 restraints weight = 36996.096| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.72 r_work: 0.2959 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21386 Z= 0.124 Angle : 0.505 12.238 28998 Z= 0.263 Chirality : 0.040 0.157 3314 Planarity : 0.004 0.044 3608 Dihedral : 7.796 74.269 3091 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.48 % Favored : 98.44 % Rotamer: Outliers : 2.80 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2508 helix: 2.60 (0.14), residues: 1438 sheet: 0.53 (0.42), residues: 159 loop : -0.15 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.007 0.001 HIS B 502 PHE 0.021 0.001 PHE A 399 TYR 0.015 0.001 TYR A 470 ARG 0.004 0.000 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 1170) hydrogen bonds : angle 3.84088 ( 3363) metal coordination : bond 0.00391 ( 7) metal coordination : angle 0.01447 ( 1) covalent geometry : bond 0.00283 (21379) covalent geometry : angle 0.50469 (28997) *********************** 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 369 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 2.311 Fit side-chains revert: symmetry clash REVERT: D 479 MET cc_start: 0.8430 (mmm) cc_final: 0.7979 (mtm) REVERT: D 532 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7680 (mtt180) REVERT: D 589 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7617 (tmtm) REVERT: A 202 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8287 (mtp85) REVERT: A 204 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8261 (mptt) REVERT: A 375 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7703 (tp30) REVERT: A 501 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 513 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 580 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8430 (ttpp) REVERT: A 588 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: A 755 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8697 (ttm) REVERT: A 780 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: A 824 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7286 (mmm160) REVERT: A 1032 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7635 (mtp) REVERT: A 1064 ASP cc_start: 0.7377 (t0) cc_final: 0.6817 (t0) REVERT: A 1078 ARG cc_start: 0.6873 (tpp-160) cc_final: 0.6574 (tmm-80) REVERT: A 1133 GLU cc_start: 0.7872 (tp30) cc_final: 0.7617 (mm-30) REVERT: A 1438 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 1442 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 1453 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7240 (p0) REVERT: A 1564 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8151 (mpt180) REVERT: A 2024 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7269 (ptpp) REVERT: A 2067 LYS cc_start: 0.8881 (tptm) cc_final: 0.8666 (ttpp) REVERT: A 2105 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 2131 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 2215 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8114 (mtmt) REVERT: B 521 ILE cc_start: 0.8743 (mm) cc_final: 0.8525 (mt) REVERT: B 665 LYS cc_start: 0.8860 (tttt) cc_final: 0.8576 (ptmt) REVERT: B 669 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8121 (mtt180) REVERT: B 676 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7521 (mt-10) REVERT: B 682 ILE cc_start: 0.8350 (mm) cc_final: 0.8119 (mp) outliers start: 65 outliers final: 37 residues processed: 339 average time/residue: 1.4855 time to fit residues: 566.6022 Evaluate side-chains 347 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 572 VAL 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 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 780 GLU 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 920 VAL Chi-restraints excluded: chain A residue 970 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 1442 GLU Chi-restraints excluded: chain A residue 1453 ASN Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2053 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 533 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 576 ILE 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 78 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3384 r_free = 0.3384 target = 0.094053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076896 restraints weight = 37114.830| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.71 r_work: 0.2939 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3170 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= 0.166 Angle : 0.539 12.385 28998 Z= 0.281 Chirality : 0.042 0.162 3314 Planarity : 0.004 0.045 3608 Dihedral : 7.875 74.362 3091 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.28 % Favored : 98.64 % Rotamer: Outliers : 2.54 % Allowed : 18.76 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.17), residues: 2508 helix: 2.49 (0.14), residues: 1439 sheet: 0.51 (0.41), residues: 171 loop : -0.19 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2234 HIS 0.007 0.001 HIS B 502 PHE 0.023 0.001 PHE A 399 TYR 0.024 0.002 TYR E 498 ARG 0.004 0.000 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 1170) hydrogen bonds : angle 3.91126 ( 3363) metal coordination : bond 0.00506 ( 7) metal coordination : angle 0.77392 ( 1) covalent geometry : bond 0.00392 (21379) covalent geometry : angle 0.53940 (28997) ********************** 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 355 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 2.370 Fit side-chains revert: symmetry clash REVERT: C 497 ASN cc_start: 0.8221 (m-40) cc_final: 0.7927 (m-40) REVERT: D 479 MET cc_start: 0.8427 (mmm) cc_final: 0.7953 (mtm) REVERT: D 532 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7728 (mtt180) REVERT: D 589 LYS cc_start: 0.7848 (tmtt) cc_final: 0.7627 (tmtm) REVERT: E 503 LEU cc_start: 0.8394 (mm) cc_final: 0.8109 (mm) REVERT: A 202 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8285 (mtp85) REVERT: A 204 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8259 (mptt) REVERT: A 375 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: A 501 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 513 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: A 588 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 755 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8712 (ttm) REVERT: A 780 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: A 824 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (mmm160) REVERT: A 1032 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7597 (mtp) REVERT: A 1064 ASP cc_start: 0.7490 (t0) cc_final: 0.6906 (t0) REVERT: A 1078 ARG cc_start: 0.6908 (tpp-160) cc_final: 0.6531 (tmm-80) REVERT: A 1096 LYS cc_start: 0.8054 (tppp) cc_final: 0.7832 (mmmm) REVERT: A 1133 GLU cc_start: 0.7881 (tp30) cc_final: 0.7644 (mm-30) REVERT: A 1438 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 1442 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 1564 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8177 (mpt180) REVERT: A 2024 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7307 (ptpp) REVERT: A 2067 LYS cc_start: 0.8898 (tptm) cc_final: 0.8660 (ttpp) REVERT: A 2105 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: A 2131 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7845 (t80) REVERT: A 2215 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8116 (mtmt) REVERT: B 521 ILE cc_start: 0.8814 (mm) cc_final: 0.8606 (mt) REVERT: B 665 LYS cc_start: 0.8892 (tttt) cc_final: 0.8614 (ptmt) REVERT: B 669 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8155 (mtt180) REVERT: B 676 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7575 (mt-10) REVERT: B 682 ILE cc_start: 0.8375 (mm) cc_final: 0.8143 (mp) outliers start: 59 outliers final: 36 residues processed: 330 average time/residue: 1.5227 time to fit residues: 565.4226 Evaluate side-chains 341 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 572 VAL 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 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 780 GLU 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 920 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1032 MET 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 1552 ILE Chi-restraints excluded: chain A residue 1564 ARG Chi-restraints excluded: chain A residue 1695 CYS Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2053 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 533 LEU Chi-restraints excluded: chain B residue 565 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 24 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 205 optimal weight: 0.0980 chunk 37 optimal weight: 0.0000 chunk 191 optimal weight: 0.7980 chunk 159 optimal weight: 0.0980 chunk 195 optimal weight: 0.6980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3412 r_free = 0.3412 target = 0.095719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078603 restraints weight = 37022.290| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.72 r_work: 0.2974 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21386 Z= 0.108 Angle : 0.500 12.115 28998 Z= 0.259 Chirality : 0.040 0.162 3314 Planarity : 0.004 0.043 3608 Dihedral : 7.736 74.158 3091 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.28 % Favored : 98.64 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.17), residues: 2508 helix: 2.67 (0.14), residues: 1438 sheet: 0.55 (0.42), residues: 159 loop : -0.11 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1248 HIS 0.008 0.001 HIS B 502 PHE 0.019 0.001 PHE A 399 TYR 0.015 0.001 TYR A 470 ARG 0.004 0.000 ARG A1180 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 1170) hydrogen bonds : angle 3.77738 ( 3363) metal coordination : bond 0.00261 ( 7) metal coordination : angle 0.50888 ( 1) covalent geometry : bond 0.00233 (21379) covalent geometry : angle 0.50016 (28997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15837.41 seconds wall clock time: 273 minutes 30.16 seconds (16410.16 seconds total)