Starting phenix.real_space_refine on Tue Jul 23 04:29:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdb_37130/07_2024/8kdb_37130_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdb_37130/07_2024/8kdb_37130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdb_37130/07_2024/8kdb_37130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdb_37130/07_2024/8kdb_37130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdb_37130/07_2024/8kdb_37130_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdb_37130/07_2024/8kdb_37130_neut.cif" } resolution = 2.7 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 108 5.16 5 C 13326 2.51 5 N 3510 2.21 5 O 3914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2063": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20861 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17081 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2117, 17065 Classifications: {'peptide': 2117} Link IDs: {'PTRANS': 73, 'TRANS': 2043} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 2117, 17065 Classifications: {'peptide': 2117} Link IDs: {'PTRANS': 73, 'TRANS': 2043} Chain breaks: 5 bond proxies already assigned to first conformer: 17395 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 510 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 335 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "E" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 279 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2039 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 6, 'TRANS': 245} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9257 SG CYS A1177 73.533 110.927 65.221 1.00 57.16 S ATOM 9280 SG CYS A1180 75.394 108.712 63.150 1.00 59.00 S ATOM 8921 SG CYS A1132 86.714 106.522 81.440 1.00 54.49 S ATOM 10728 SG CYS A1371 85.257 108.241 78.329 1.00 76.37 S ATOM 10734 SG CYS A1372 83.697 105.468 79.652 1.00 65.43 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASN A 347 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 347 " occ=0.50 residue: pdb=" N AMET A 472 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 472 " occ=0.50 Time building chain proxies: 17.71, per 1000 atoms: 0.85 Number of scatterers: 20861 At special positions: 0 Unit cell: (123.918, 143.484, 169.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 108 16.00 Mg 1 11.99 O 3914 8.00 N 3510 7.00 C 13326 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 - 3.50 Amino acid : False - 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: 6.87 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" ND1 HIS A1364 " pdb="ZN ZN A3002 " - pdb=" NE2 HIS A1366 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1180 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1177 " pdb=" ZN A3003 " pdb="ZN ZN A3003 " - pdb=" SG CYS A1372 " pdb="ZN ZN A3003 " - pdb=" SG CYS A1132 " pdb="ZN ZN A3003 " - pdb=" SG CYS A1371 " Number of angles added : 2 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4938 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 59.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.693A pdb=" N LEU A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 Processing helix chain 'A' and resid 151 through 166 removed outlier: 4.018A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N HIS A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.765A pdb=" N ASN A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.770A pdb=" N GLN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.866A pdb=" N VAL A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.640A pdb=" N LYS A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.852A pdb=" N PHE A 361 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.767A pdb=" N LYS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 448 through 451 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 517 through 527 removed outlier: 3.996A pdb=" N ILE A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 588 through 602 Processing helix chain 'A' and resid 672 through 688 removed outlier: 3.511A pdb=" N THR A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 721 through 724 Processing helix chain 'A' and resid 744 through 762 removed outlier: 4.128A pdb=" N ILE A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.780A pdb=" N LYS A 798 " --> pdb=" O GLU A 794 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 864 through 881 Processing helix chain 'A' and resid 884 through 906 Processing helix chain 'A' and resid 914 through 923 Processing helix chain 'A' and resid 925 through 933 Processing helix chain 'A' and resid 944 through 949 Processing helix chain 'A' and resid 956 through 970 Processing helix chain 'A' and resid 975 through 983 Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1008 through 1020 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1037 through 1051 Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.682A pdb=" N ASN A1066 " --> pdb=" O ASP A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1077 Processing helix chain 'A' and resid 1081 through 1093 Processing helix chain 'A' and resid 1096 through 1105 removed outlier: 4.544A pdb=" N LYS A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1119 Processing helix chain 'A' and resid 1127 through 1131 Processing helix chain 'A' and resid 1132 through 1145 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1161 through 1165 Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1234 through 1251 Processing helix chain 'A' and resid 1254 through 1266 Processing helix chain 'A' and resid 1272 through 1280 Processing helix chain 'A' and resid 1331 through 1350 Processing helix chain 'A' and resid 1410 through 1424 Processing helix chain 'A' and resid 1430 through 1456 removed outlier: 3.947A pdb=" N ARG A1455 " --> pdb=" O SER A1451 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A1456 " --> pdb=" O GLN A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1463 Processing helix chain 'A' and resid 1473 through 1480 Processing helix chain 'A' and resid 1481 through 1504 removed outlier: 4.954A pdb=" N TYR A1499 " --> pdb=" O ASN A1495 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR A1500 " --> pdb=" O GLN A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1523 Processing helix chain 'A' and resid 1528 through 1536 Processing helix chain 'A' and resid 1538 through 1546 Processing helix chain 'A' and resid 1562 through 1585 Processing helix chain 'A' and resid 1596 through 1619 removed outlier: 3.603A pdb=" N GLN A1605 " --> pdb=" O ASN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1625 Processing helix chain 'A' and resid 1632 through 1651 Processing helix chain 'A' and resid 1670 through 1686 Processing helix chain 'A' and resid 1709 through 1724 Processing helix chain 'A' and resid 1769 through 1775 Processing helix chain 'A' and resid 1785 through 1798 removed outlier: 4.665A pdb=" N GLN A1792 " --> pdb=" O LEU A1788 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A1793 " --> pdb=" O GLU A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1822 Processing helix chain 'A' and resid 1834 through 1838 Processing helix chain 'A' and resid 1849 through 1859 Processing helix chain 'A' and resid 1863 through 1866 Processing helix chain 'A' and resid 1875 through 1879 Processing helix chain 'A' and resid 1884 through 1895 Processing helix chain 'A' and resid 1913 through 1931 Processing helix chain 'A' and resid 1951 through 1961 Processing helix chain 'A' and resid 1994 through 2001 Processing helix chain 'A' and resid 2005 through 2037 Processing helix chain 'A' and resid 2042 through 2052 Processing helix chain 'A' and resid 2056 through 2065 Processing helix chain 'A' and resid 2073 through 2094 Processing helix chain 'A' and resid 2115 through 2140 Processing helix chain 'A' and resid 2147 through 2155 Processing helix chain 'A' and resid 2161 through 2166 Processing helix chain 'A' and resid 2172 through 2181 removed outlier: 3.524A pdb=" N CYS A2181 " --> pdb=" O ASN A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2208 removed outlier: 3.688A pdb=" N ILE A2196 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.604A pdb=" N LYS B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS B 581 " --> pdb=" O ASN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'C' and resid 435 through 469 Processing helix chain 'D' and resid 435 through 462 Processing helix chain 'E' and resid 435 through 469 Processing helix chain 'F' and resid 435 through 463 Processing helix chain 'G' and resid 1430 through 1447 Processing helix chain 'G' and resid 1449 through 1458 Processing helix chain 'G' and resid 1474 through 1479 Processing helix chain 'G' and resid 1481 through 1504 removed outlier: 3.598A pdb=" N PHE G1497 " --> pdb=" O LEU G1493 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR G1499 " --> pdb=" O ASN G1495 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR G1500 " --> pdb=" O GLN G1496 " (cutoff:3.500A) Processing helix chain 'G' and resid 1508 through 1523 Processing helix chain 'G' and resid 1526 through 1536 Processing helix chain 'G' and resid 1538 through 1548 Processing helix chain 'G' and resid 1563 through 1584 removed outlier: 3.520A pdb=" N ASP G1576 " --> pdb=" O GLU G1572 " (cutoff:3.500A) Processing helix chain 'G' and resid 1596 through 1619 Processing helix chain 'G' and resid 1632 through 1651 Processing helix chain 'G' and resid 1670 through 1685 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.507A pdb=" N THR A 87 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU A 230 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 389 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 557 removed outlier: 5.172A pdb=" N ILE A 538 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 706 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 644 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 771 removed outlier: 4.217A pdb=" N ARG A 765 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 829 through 832 Processing sheet with id=AA8, first strand: chain 'A' and resid 1054 through 1055 Processing sheet with id=AA9, first strand: chain 'A' and resid 1166 through 1171 removed outlier: 4.034A pdb=" N VAL A1362 " --> pdb=" O ILE A1171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1588 through 1593 Processing sheet with id=AB2, first strand: chain 'A' and resid 1738 through 1740 removed outlier: 3.682A pdb=" N LYS A1941 " --> pdb=" O CYS A1904 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP A1803 " --> pdb=" O ILE A1899 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1901 " --> pdb=" O ASP A1803 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A1804 " --> pdb=" O TYR A1828 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN A1830 " --> pdb=" O ARG A1804 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE A1806 " --> pdb=" O ASN A1830 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 1588 through 1593 removed outlier: 6.477A pdb=" N LEU G1588 " --> pdb=" O LEU G1663 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS G1665 " --> pdb=" O LEU G1588 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE G1590 " --> pdb=" O LYS G1665 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N PHE G1667 " --> pdb=" O ILE G1590 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE G1592 " --> pdb=" O PHE G1667 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1168 hydrogen bonds defined for protein. 3387 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: 8.85 Time building geometry restraints manager: 7.71 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: 6532 1.34 - 1.45: 2715 1.45 - 1.57: 11827 1.57 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 21250 Sorted by residual: bond pdb=" CA ASN D 463 " pdb=" CB ASN D 463 " ideal model delta sigma weight residual 1.526 1.570 -0.044 1.76e-02 3.23e+03 6.25e+00 bond pdb=" CB VAL A1494 " pdb=" CG1 VAL A1494 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CD GLU D 441 " pdb=" OE1 GLU D 441 " ideal model delta sigma weight residual 1.249 1.231 0.018 1.90e-02 2.77e+03 8.95e-01 bond pdb=" C PHE A1215 " pdb=" N GLY A1216 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.33e-01 bond pdb=" CB VAL A 525 " pdb=" CG2 VAL A 525 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.23e-01 ... (remaining 21245 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.54: 331 105.54 - 112.67: 11391 112.67 - 119.80: 7083 119.80 - 126.93: 9701 126.93 - 134.06: 221 Bond angle restraints: 28727 Sorted by residual: angle pdb=" N GLU C 448 " pdb=" CA GLU C 448 " pdb=" CB GLU C 448 " ideal model delta sigma weight residual 110.28 115.57 -5.29 1.55e+00 4.16e-01 1.16e+01 angle pdb=" N GLU D 441 " pdb=" CA GLU D 441 " pdb=" CB GLU D 441 " ideal model delta sigma weight residual 110.16 114.98 -4.82 1.48e+00 4.57e-01 1.06e+01 angle pdb=" C LYS A2062 " pdb=" N GLU A2063 " pdb=" CA GLU A2063 " ideal model delta sigma weight residual 122.65 117.66 4.99 1.60e+00 3.91e-01 9.71e+00 angle pdb=" C ASN A 690 " pdb=" N LYS A 691 " pdb=" CA LYS A 691 " ideal model delta sigma weight residual 122.61 127.27 -4.66 1.56e+00 4.11e-01 8.91e+00 angle pdb=" C ASN A 650 " pdb=" N ASP A 651 " pdb=" CA ASP A 651 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.54e+00 ... (remaining 28722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11754 17.76 - 35.52: 990 35.52 - 53.29: 149 53.29 - 71.05: 31 71.05 - 88.81: 13 Dihedral angle restraints: 12937 sinusoidal: 5316 harmonic: 7621 Sorted by residual: dihedral pdb=" CA CYS A 658 " pdb=" C CYS A 658 " pdb=" N PHE A 659 " pdb=" CA PHE A 659 " ideal model delta harmonic sigma weight residual 180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS A1796 " pdb=" C LYS A1796 " pdb=" N GLU A1797 " pdb=" CA GLU A1797 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR A 662 " pdb=" C THR A 662 " pdb=" N ASP A 663 " pdb=" CA ASP A 663 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 12934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2271 0.037 - 0.074: 766 0.074 - 0.111: 195 0.111 - 0.148: 49 0.148 - 0.185: 4 Chirality restraints: 3285 Sorted by residual: chirality pdb=" CA GLU A2063 " pdb=" N GLU A2063 " pdb=" C GLU A2063 " pdb=" CB GLU A2063 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA TYR A 91 " pdb=" N TYR A 91 " pdb=" C TYR A 91 " pdb=" CB TYR A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA GLU D 441 " pdb=" N GLU D 441 " pdb=" C GLU D 441 " pdb=" CB GLU D 441 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 3282 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 985 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 986 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 444 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ARG C 444 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG C 444 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG C 445 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G1643 " -0.011 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR G1643 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR G1643 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G1643 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR G1643 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G1643 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G1643 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G1643 " 0.000 2.00e-02 2.50e+03 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 132 2.58 - 3.16: 16972 3.16 - 3.74: 31419 3.74 - 4.32: 44000 4.32 - 4.90: 74820 Nonbonded interactions: 167343 Sorted by model distance: nonbonded pdb=" OE2 GLU A1164 " pdb="ZN ZN A3003 " model vdw 1.999 2.230 nonbonded pdb=" OD2 ASP A 773 " pdb="MG MG A3001 " model vdw 2.063 2.170 nonbonded pdb=" O THR A1862 " pdb=" NH1 ARG A1867 " model vdw 2.226 2.520 nonbonded pdb=" OH TYR A 797 " pdb=" O THR B 544 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASP C 440 " pdb=" NE2 HIS F 443 " model vdw 2.259 2.520 ... (remaining 167338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 435 through 467) selection = (chain 'D' and resid 435 through 467) selection = (chain 'E' and resid 435 through 467) selection = (chain 'F' and resid 435 through 467) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.190 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: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 68.430 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21250 Z= 0.176 Angle : 0.525 8.735 28727 Z= 0.285 Chirality : 0.040 0.185 3285 Planarity : 0.004 0.044 3620 Dihedral : 13.326 88.809 7999 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.87 % 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: 1.35 (0.17), residues: 2564 helix: 2.00 (0.14), residues: 1457 sheet: 0.27 (0.38), residues: 197 loop : -0.80 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G1545 HIS 0.012 0.001 HIS A2059 PHE 0.022 0.001 PHE A 361 TYR 0.027 0.001 TYR G1643 ARG 0.009 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: A 1426 MET cc_start: 0.8966 (mtt) cc_final: 0.8694 (mtm) REVERT: A 1728 PHE cc_start: 0.8291 (m-80) cc_final: 0.8088 (m-80) REVERT: B 545 ARG cc_start: 0.8089 (ptt-90) cc_final: 0.7826 (pmt170) REVERT: B 597 GLU cc_start: 0.7865 (tp30) cc_final: 0.7512 (tp30) REVERT: D 452 GLU cc_start: 0.8133 (tp30) cc_final: 0.7927 (tp30) REVERT: G 1450 MET cc_start: 0.7206 (mmm) cc_final: 0.6945 (mmm) REVERT: G 1455 ARG cc_start: 0.7227 (mtm180) cc_final: 0.6689 (mmt-90) REVERT: G 1597 MET cc_start: 0.6447 (tpt) cc_final: 0.6150 (tpt) REVERT: G 1624 PHE cc_start: 0.8240 (m-10) cc_final: 0.7974 (m-80) REVERT: G 1663 LEU cc_start: 0.7835 (tt) cc_final: 0.7620 (tt) REVERT: G 1673 TYR cc_start: 0.7704 (t80) cc_final: 0.7492 (t80) outliers start: 1 outliers final: 4 residues processed: 325 average time/residue: 1.4054 time to fit residues: 514.1617 Evaluate side-chains 249 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain G residue 1633 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 387 GLN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 774 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1647 ASN A1735 ASN ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN C 450 GLN E 449 ASN ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21250 Z= 0.336 Angle : 0.589 9.772 28727 Z= 0.309 Chirality : 0.043 0.169 3285 Planarity : 0.004 0.075 3620 Dihedral : 4.637 57.104 2815 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.44 % Allowed : 7.59 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.17), residues: 2564 helix: 2.03 (0.14), residues: 1476 sheet: 0.16 (0.37), residues: 197 loop : -0.84 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1545 HIS 0.005 0.001 HIS A 756 PHE 0.021 0.002 PHE A 400 TYR 0.021 0.002 TYR A1422 ARG 0.006 0.001 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: A 362 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7961 (mmt-90) REVERT: A 945 MET cc_start: 0.8734 (mtp) cc_final: 0.8487 (mtp) REVERT: A 1426 MET cc_start: 0.8969 (mtt) cc_final: 0.8676 (mtm) REVERT: A 2025 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: A 2078 GLN cc_start: 0.8993 (mp10) cc_final: 0.8393 (mp10) REVERT: B 545 ARG cc_start: 0.8106 (ptt-90) cc_final: 0.7800 (pmt170) REVERT: B 597 GLU cc_start: 0.7799 (tp30) cc_final: 0.7433 (tp30) REVERT: D 452 GLU cc_start: 0.8106 (tp30) cc_final: 0.7874 (tp30) REVERT: G 1455 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6804 (mmt-90) REVERT: G 1597 MET cc_start: 0.6324 (tpt) cc_final: 0.6098 (tpt) REVERT: G 1624 PHE cc_start: 0.8220 (m-10) cc_final: 0.7942 (m-80) REVERT: G 1649 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7639 (ttpt) REVERT: G 1663 LEU cc_start: 0.7887 (tt) cc_final: 0.7649 (tt) REVERT: G 1673 TYR cc_start: 0.7724 (t80) cc_final: 0.7486 (t80) outliers start: 34 outliers final: 14 residues processed: 273 average time/residue: 1.3063 time to fit residues: 405.7963 Evaluate side-chains 264 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 247 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 1274 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1470 ILE Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1966 ILE Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2161 ASP Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1649 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 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 21 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1735 ASN ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2093 ASN A2153 GLN B 600 ASN C 450 GLN ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21250 Z= 0.207 Angle : 0.516 9.987 28727 Z= 0.270 Chirality : 0.040 0.152 3285 Planarity : 0.003 0.041 3620 Dihedral : 4.237 38.926 2811 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.48 % Allowed : 8.91 % Favored : 89.61 % 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: 1.61 (0.17), residues: 2564 helix: 2.25 (0.14), residues: 1478 sheet: 0.19 (0.37), residues: 197 loop : -0.79 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G1545 HIS 0.003 0.001 HIS A 161 PHE 0.018 0.001 PHE A 400 TYR 0.012 0.001 TYR A 524 ARG 0.007 0.000 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 266 time to evaluate : 2.896 Fit side-chains REVERT: A 320 MET cc_start: 0.8897 (mtm) cc_final: 0.8553 (mtt) REVERT: A 362 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7947 (mmt-90) REVERT: A 377 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7820 (mmtp) REVERT: A 391 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7094 (p0) REVERT: A 945 MET cc_start: 0.8715 (mtp) cc_final: 0.8485 (mtp) REVERT: A 1426 MET cc_start: 0.8973 (mtt) cc_final: 0.8680 (mtm) REVERT: A 2025 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 2046 MET cc_start: 0.7642 (mmm) cc_final: 0.7429 (mmt) REVERT: A 2078 GLN cc_start: 0.8989 (mp10) cc_final: 0.8301 (mp10) REVERT: B 597 GLU cc_start: 0.7787 (tp30) cc_final: 0.7415 (tp30) REVERT: C 465 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8487 (ttmt) REVERT: D 452 GLU cc_start: 0.8111 (tp30) cc_final: 0.7872 (tp30) REVERT: F 467 MET cc_start: 0.5683 (mmm) cc_final: 0.5430 (mmp) REVERT: G 1455 ARG cc_start: 0.7164 (mtm180) cc_final: 0.6857 (mmt-90) REVERT: G 1597 MET cc_start: 0.6353 (tpt) cc_final: 0.6087 (tpt) REVERT: G 1624 PHE cc_start: 0.8234 (m-10) cc_final: 0.7977 (m-80) REVERT: G 1649 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7624 (ptpp) REVERT: G 1663 LEU cc_start: 0.7988 (tt) cc_final: 0.7722 (tt) REVERT: G 1673 TYR cc_start: 0.7712 (t80) cc_final: 0.7507 (t80) outliers start: 35 outliers final: 13 residues processed: 283 average time/residue: 1.3242 time to fit residues: 427.8029 Evaluate side-chains 273 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 256 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 1274 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1470 ILE Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2132 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1633 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 214 HIS ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1735 ASN ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN C 450 GLN ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21250 Z= 0.391 Angle : 0.605 11.187 28727 Z= 0.316 Chirality : 0.044 0.182 3285 Planarity : 0.004 0.086 3620 Dihedral : 4.385 40.307 2809 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.91 % Allowed : 9.88 % Favored : 88.21 % 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: 1.43 (0.17), residues: 2564 helix: 2.12 (0.13), residues: 1467 sheet: 0.14 (0.37), residues: 198 loop : -0.87 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G1545 HIS 0.006 0.001 HIS A 756 PHE 0.023 0.002 PHE A 400 TYR 0.015 0.002 TYR A 524 ARG 0.008 0.001 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 2.294 Fit side-chains REVERT: A 362 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7966 (mmt-90) REVERT: A 391 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7132 (p0) REVERT: A 771 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: A 945 MET cc_start: 0.8753 (mtp) cc_final: 0.8313 (mtp) REVERT: A 1038 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8084 (ptt) REVERT: A 1426 MET cc_start: 0.8959 (mtt) cc_final: 0.8662 (mtm) REVERT: A 2025 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: A 2078 GLN cc_start: 0.8997 (mp10) cc_final: 0.8317 (mp10) REVERT: B 597 GLU cc_start: 0.7905 (tp30) cc_final: 0.7492 (tp30) REVERT: C 448 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: C 465 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8481 (ttmt) REVERT: D 452 GLU cc_start: 0.8095 (tp30) cc_final: 0.7847 (tp30) REVERT: F 467 MET cc_start: 0.5725 (mmm) cc_final: 0.5387 (mmp) REVERT: G 1455 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6839 (mmt-90) REVERT: G 1597 MET cc_start: 0.6390 (tpt) cc_final: 0.6144 (tpt) REVERT: G 1624 PHE cc_start: 0.8263 (m-10) cc_final: 0.7949 (m-80) REVERT: G 1649 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7614 (ptpp) REVERT: G 1663 LEU cc_start: 0.8044 (tt) cc_final: 0.7800 (tt) REVERT: G 1673 TYR cc_start: 0.7680 (t80) cc_final: 0.7456 (t80) outliers start: 45 outliers final: 23 residues processed: 278 average time/residue: 1.3145 time to fit residues: 416.8401 Evaluate side-chains 279 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 249 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1274 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1470 ILE Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2132 LEU Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain A residue 2161 ASP Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1547 CYS Chi-restraints excluded: chain G residue 1633 TYR Chi-restraints excluded: chain G residue 1646 LEU Chi-restraints excluded: chain G residue 1649 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1715 ASN ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21250 Z= 0.179 Angle : 0.511 11.968 28727 Z= 0.268 Chirality : 0.039 0.139 3285 Planarity : 0.003 0.040 3620 Dihedral : 4.123 37.938 2809 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.44 % Allowed : 10.73 % Favored : 87.83 % 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: 1.66 (0.17), residues: 2564 helix: 2.33 (0.14), residues: 1474 sheet: 0.21 (0.37), residues: 202 loop : -0.83 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G1545 HIS 0.003 0.001 HIS A 214 PHE 0.017 0.001 PHE A 173 TYR 0.017 0.001 TYR G1633 ARG 0.011 0.000 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 2.452 Fit side-chains revert: symmetry clash REVERT: A 320 MET cc_start: 0.8917 (mtm) cc_final: 0.8522 (mtt) REVERT: A 377 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7865 (mmtp) REVERT: A 771 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6788 (pt0) REVERT: A 945 MET cc_start: 0.8704 (mtp) cc_final: 0.8377 (mtp) REVERT: A 1038 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7982 (ptt) REVERT: A 1426 MET cc_start: 0.8962 (mtt) cc_final: 0.8663 (mtm) REVERT: A 1602 ASP cc_start: 0.7946 (m-30) cc_final: 0.7726 (m-30) REVERT: A 1728 PHE cc_start: 0.8274 (m-80) cc_final: 0.8066 (m-80) REVERT: A 2025 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: A 2046 MET cc_start: 0.7624 (mmm) cc_final: 0.7417 (mmt) REVERT: B 597 GLU cc_start: 0.7882 (tp30) cc_final: 0.7462 (tp30) REVERT: C 448 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 465 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8523 (ttmt) REVERT: D 452 GLU cc_start: 0.8097 (tp30) cc_final: 0.7760 (tp30) REVERT: E 439 MET cc_start: 0.5166 (OUTLIER) cc_final: 0.4881 (ptm) REVERT: F 467 MET cc_start: 0.5658 (mmm) cc_final: 0.5406 (mmp) REVERT: G 1597 MET cc_start: 0.6417 (tpt) cc_final: 0.6154 (tpt) REVERT: G 1624 PHE cc_start: 0.8260 (m-10) cc_final: 0.7976 (m-80) REVERT: G 1649 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7635 (ptpp) REVERT: G 1663 LEU cc_start: 0.8097 (tt) cc_final: 0.7822 (tt) REVERT: G 1673 TYR cc_start: 0.7673 (t80) cc_final: 0.7471 (t80) outliers start: 34 outliers final: 15 residues processed: 284 average time/residue: 1.3726 time to fit residues: 443.1168 Evaluate side-chains 276 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1274 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1470 ILE Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain A residue 2161 ASP Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1475 THR Chi-restraints excluded: chain G residue 1547 CYS Chi-restraints excluded: chain G residue 1633 TYR Chi-restraints excluded: chain G residue 1646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 114 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 129 optimal weight: 0.8980 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 151 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 HIS F 453 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21250 Z= 0.199 Angle : 0.514 13.390 28727 Z= 0.266 Chirality : 0.040 0.154 3285 Planarity : 0.003 0.052 3620 Dihedral : 4.045 37.705 2809 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.65 % Allowed : 11.11 % Favored : 87.23 % 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: 1.75 (0.17), residues: 2564 helix: 2.40 (0.14), residues: 1474 sheet: 0.23 (0.37), residues: 202 loop : -0.80 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G1545 HIS 0.003 0.001 HIS A 214 PHE 0.019 0.001 PHE A 400 TYR 0.012 0.001 TYR A 524 ARG 0.012 0.000 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 2.329 Fit side-chains REVERT: A 150 LEU cc_start: 0.7354 (mp) cc_final: 0.7146 (tt) REVERT: A 320 MET cc_start: 0.8908 (mtm) cc_final: 0.8534 (mtt) REVERT: A 377 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7935 (mmtp) REVERT: A 771 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7078 (pt0) REVERT: A 945 MET cc_start: 0.8718 (mtp) cc_final: 0.8328 (mtp) REVERT: A 1038 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7947 (ptt) REVERT: A 1426 MET cc_start: 0.8976 (mtt) cc_final: 0.8706 (mtm) REVERT: A 1728 PHE cc_start: 0.8282 (m-80) cc_final: 0.8057 (m-80) REVERT: A 2025 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: A 2046 MET cc_start: 0.7626 (mmm) cc_final: 0.7401 (mmt) REVERT: B 597 GLU cc_start: 0.7904 (tp30) cc_final: 0.7467 (tp30) REVERT: C 439 MET cc_start: 0.4481 (OUTLIER) cc_final: 0.4053 (ttp) REVERT: C 448 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: D 452 GLU cc_start: 0.8095 (tp30) cc_final: 0.7760 (tp30) REVERT: E 439 MET cc_start: 0.5028 (OUTLIER) cc_final: 0.4728 (ptm) REVERT: F 467 MET cc_start: 0.5691 (mmm) cc_final: 0.5446 (mmp) REVERT: G 1455 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7118 (mmt-90) REVERT: G 1597 MET cc_start: 0.6431 (tpt) cc_final: 0.6203 (tpt) REVERT: G 1624 PHE cc_start: 0.8265 (m-10) cc_final: 0.7973 (m-80) REVERT: G 1649 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7609 (ptpp) REVERT: G 1663 LEU cc_start: 0.8118 (tt) cc_final: 0.7840 (tt) REVERT: G 1673 TYR cc_start: 0.7652 (t80) cc_final: 0.7450 (t80) outliers start: 39 outliers final: 20 residues processed: 279 average time/residue: 1.3119 time to fit residues: 420.0065 Evaluate side-chains 286 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1274 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1470 ILE Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1547 CYS Chi-restraints excluded: chain G residue 1632 THR Chi-restraints excluded: chain G residue 1646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 HIS F 453 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21250 Z= 0.206 Angle : 0.516 13.732 28727 Z= 0.267 Chirality : 0.040 0.151 3285 Planarity : 0.004 0.059 3620 Dihedral : 4.047 39.631 2809 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.70 % Allowed : 11.32 % Favored : 86.98 % 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: 1.75 (0.17), residues: 2564 helix: 2.41 (0.13), residues: 1475 sheet: 0.23 (0.37), residues: 202 loop : -0.80 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G1545 HIS 0.003 0.001 HIS A 161 PHE 0.019 0.001 PHE A 400 TYR 0.029 0.001 TYR G1643 ARG 0.012 0.000 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 263 time to evaluate : 2.408 Fit side-chains REVERT: A 320 MET cc_start: 0.8907 (mtm) cc_final: 0.8538 (mtt) REVERT: A 377 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7945 (mmtp) REVERT: A 771 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7089 (pt0) REVERT: A 945 MET cc_start: 0.8731 (mtp) cc_final: 0.8321 (mtp) REVERT: A 1038 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7983 (ptt) REVERT: A 1408 ASP cc_start: 0.7521 (p0) cc_final: 0.7258 (p0) REVERT: A 1426 MET cc_start: 0.8984 (mtt) cc_final: 0.8726 (mtm) REVERT: A 1728 PHE cc_start: 0.8279 (m-80) cc_final: 0.8051 (m-80) REVERT: A 2025 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: A 2046 MET cc_start: 0.7600 (mmm) cc_final: 0.7384 (mmt) REVERT: B 597 GLU cc_start: 0.7894 (tp30) cc_final: 0.7459 (tp30) REVERT: C 448 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: C 465 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8580 (ttpt) REVERT: D 452 GLU cc_start: 0.8193 (tp30) cc_final: 0.7865 (tp30) REVERT: E 439 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4757 (ptm) REVERT: G 1597 MET cc_start: 0.6406 (tpt) cc_final: 0.6164 (tpt) REVERT: G 1624 PHE cc_start: 0.8266 (m-10) cc_final: 0.7965 (m-80) REVERT: G 1649 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7611 (ptpp) REVERT: G 1663 LEU cc_start: 0.8141 (tt) cc_final: 0.7853 (tt) REVERT: G 1673 TYR cc_start: 0.7580 (t80) cc_final: 0.7363 (t80) outliers start: 40 outliers final: 26 residues processed: 282 average time/residue: 1.2693 time to fit residues: 409.6506 Evaluate side-chains 286 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1274 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1470 ILE Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain A residue 2190 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1475 THR Chi-restraints excluded: chain G residue 1547 CYS Chi-restraints excluded: chain G residue 1632 THR Chi-restraints excluded: chain G residue 1633 TYR Chi-restraints excluded: chain G residue 1646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN E 450 GLN F 443 HIS F 453 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21250 Z= 0.152 Angle : 0.497 14.030 28727 Z= 0.256 Chirality : 0.039 0.141 3285 Planarity : 0.003 0.059 3620 Dihedral : 3.938 38.738 2809 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.61 % Allowed : 11.75 % Favored : 86.64 % 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: 1.89 (0.17), residues: 2564 helix: 2.52 (0.14), residues: 1472 sheet: 0.29 (0.37), residues: 202 loop : -0.73 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G1545 HIS 0.002 0.001 HIS A1921 PHE 0.017 0.001 PHE A 400 TYR 0.031 0.001 TYR G1643 ARG 0.012 0.000 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 2.324 Fit side-chains REVERT: A 320 MET cc_start: 0.8908 (mtm) cc_final: 0.8490 (mtt) REVERT: A 377 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7913 (mmtp) REVERT: A 552 ARG cc_start: 0.6906 (mmp-170) cc_final: 0.6411 (mmt90) REVERT: A 771 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: A 945 MET cc_start: 0.8701 (mtp) cc_final: 0.8334 (mtp) REVERT: A 1038 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7891 (ptt) REVERT: A 1408 ASP cc_start: 0.7554 (p0) cc_final: 0.7316 (p0) REVERT: A 1426 MET cc_start: 0.8952 (mtt) cc_final: 0.8656 (mtm) REVERT: A 1728 PHE cc_start: 0.8240 (m-80) cc_final: 0.8019 (m-80) REVERT: A 2025 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: A 2046 MET cc_start: 0.7587 (mmm) cc_final: 0.7366 (mmt) REVERT: C 439 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.3875 (ttm) REVERT: C 448 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: D 452 GLU cc_start: 0.8194 (tp30) cc_final: 0.7857 (tp30) REVERT: E 439 MET cc_start: 0.5035 (OUTLIER) cc_final: 0.4725 (ptm) REVERT: G 1455 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6744 (mtm180) REVERT: G 1597 MET cc_start: 0.6364 (tpt) cc_final: 0.6125 (tpt) REVERT: G 1624 PHE cc_start: 0.8262 (m-10) cc_final: 0.7936 (m-80) REVERT: G 1649 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7613 (ptpp) REVERT: G 1663 LEU cc_start: 0.8161 (tt) cc_final: 0.7867 (tt) outliers start: 38 outliers final: 20 residues processed: 279 average time/residue: 1.3287 time to fit residues: 423.5660 Evaluate side-chains 273 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1245 MET Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1475 THR Chi-restraints excluded: chain G residue 1477 PHE Chi-restraints excluded: chain G residue 1547 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 99 optimal weight: 0.0030 chunk 179 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 overall best weight: 0.5148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN B 600 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN E 450 GLN F 443 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21250 Z= 0.145 Angle : 0.501 14.179 28727 Z= 0.255 Chirality : 0.039 0.205 3285 Planarity : 0.003 0.038 3620 Dihedral : 3.825 37.642 2809 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.23 % Allowed : 12.43 % Favored : 86.34 % 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: 2.01 (0.17), residues: 2564 helix: 2.58 (0.14), residues: 1478 sheet: 0.35 (0.37), residues: 200 loop : -0.63 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1545 HIS 0.003 0.001 HIS A1921 PHE 0.018 0.001 PHE A 400 TYR 0.031 0.001 TYR G1643 ARG 0.008 0.000 ARG F 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 2.439 Fit side-chains REVERT: A 320 MET cc_start: 0.8902 (mtm) cc_final: 0.8458 (mtt) REVERT: A 552 ARG cc_start: 0.6936 (mmp-170) cc_final: 0.6434 (mmt90) REVERT: A 945 MET cc_start: 0.8686 (mtp) cc_final: 0.8323 (mtp) REVERT: A 1038 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7827 (ptt) REVERT: A 1408 ASP cc_start: 0.7537 (p0) cc_final: 0.7314 (p0) REVERT: A 1426 MET cc_start: 0.8961 (mtt) cc_final: 0.8684 (mtm) REVERT: A 1728 PHE cc_start: 0.8219 (m-80) cc_final: 0.8016 (m-80) REVERT: A 2025 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 2046 MET cc_start: 0.7593 (mmm) cc_final: 0.7382 (mmt) REVERT: A 2145 ASP cc_start: 0.8054 (t0) cc_final: 0.7616 (t0) REVERT: B 597 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7442 (tp30) REVERT: C 439 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.3829 (ttm) REVERT: C 448 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 451 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8002 (ttp80) REVERT: D 452 GLU cc_start: 0.8198 (tp30) cc_final: 0.7868 (tp30) REVERT: E 439 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4526 (ptm) REVERT: G 1455 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.6918 (mtm180) REVERT: G 1597 MET cc_start: 0.6264 (tpt) cc_final: 0.5952 (tpt) REVERT: G 1624 PHE cc_start: 0.8257 (m-10) cc_final: 0.7934 (m-80) REVERT: G 1663 LEU cc_start: 0.8162 (tt) cc_final: 0.7869 (tt) outliers start: 29 outliers final: 16 residues processed: 272 average time/residue: 1.3056 time to fit residues: 404.9051 Evaluate side-chains 269 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2025 GLU Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1475 THR Chi-restraints excluded: chain G residue 1547 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 114 optimal weight: 0.0060 chunk 168 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 233 optimal weight: 0.0270 chunk 202 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 0.0040 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 549 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN A2153 GLN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN E 450 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21250 Z= 0.134 Angle : 0.490 14.207 28727 Z= 0.248 Chirality : 0.038 0.172 3285 Planarity : 0.003 0.037 3620 Dihedral : 3.715 35.504 2809 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.15 % Allowed : 12.81 % Favored : 86.05 % 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: 2.09 (0.17), residues: 2564 helix: 2.66 (0.14), residues: 1478 sheet: 0.36 (0.37), residues: 202 loop : -0.62 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G1545 HIS 0.003 0.000 HIS A1921 PHE 0.017 0.001 PHE A 400 TYR 0.030 0.001 TYR G1643 ARG 0.009 0.000 ARG F 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 2.436 Fit side-chains revert: symmetry clash REVERT: A 320 MET cc_start: 0.8890 (mtm) cc_final: 0.8537 (mtt) REVERT: A 552 ARG cc_start: 0.6900 (mmp-170) cc_final: 0.6389 (mmt90) REVERT: A 945 MET cc_start: 0.8676 (mtp) cc_final: 0.8334 (mtp) REVERT: A 1038 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7791 (ptt) REVERT: A 1408 ASP cc_start: 0.7554 (p0) cc_final: 0.7238 (p0) REVERT: A 1426 MET cc_start: 0.8938 (mtt) cc_final: 0.8684 (mtm) REVERT: A 2046 MET cc_start: 0.7653 (mmm) cc_final: 0.7446 (mmt) REVERT: A 2082 ARG cc_start: 0.8325 (mtt180) cc_final: 0.8056 (mpt180) REVERT: A 2145 ASP cc_start: 0.8043 (t0) cc_final: 0.7588 (t0) REVERT: B 597 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 439 MET cc_start: 0.4427 (OUTLIER) cc_final: 0.3875 (ttm) REVERT: C 448 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: C 451 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7952 (ttp80) REVERT: D 452 GLU cc_start: 0.8254 (tp30) cc_final: 0.7914 (tp30) REVERT: E 439 MET cc_start: 0.4982 (OUTLIER) cc_final: 0.4559 (ptm) REVERT: G 1455 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7146 (mmt-90) REVERT: G 1597 MET cc_start: 0.6273 (tpt) cc_final: 0.5983 (tpt) REVERT: G 1624 PHE cc_start: 0.8271 (m-10) cc_final: 0.7953 (m-80) REVERT: G 1663 LEU cc_start: 0.8150 (tt) cc_final: 0.7847 (tt) outliers start: 27 outliers final: 16 residues processed: 267 average time/residue: 1.4238 time to fit residues: 435.3010 Evaluate side-chains 266 residues out of total 2354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1410 ASP Chi-restraints excluded: chain A residue 1494 VAL Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2150 HIS Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 467 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 439 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 1456 ASP Chi-restraints excluded: chain G residue 1475 THR Chi-restraints excluded: chain G residue 1477 PHE Chi-restraints excluded: chain G residue 1547 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 0.3980 chunk 215 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1735 ASN ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2010 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 449 ASN E 450 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.078279 restraints weight = 62939.990| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.30 r_work: 0.2817 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21250 Z= 0.160 Angle : 0.501 14.162 28727 Z= 0.254 Chirality : 0.039 0.165 3285 Planarity : 0.003 0.037 3620 Dihedral : 3.736 36.025 2809 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.98 % Allowed : 13.23 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.17), residues: 2564 helix: 2.62 (0.14), residues: 1484 sheet: 0.38 (0.37), residues: 202 loop : -0.65 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G1545 HIS 0.003 0.001 HIS A1921 PHE 0.024 0.001 PHE G1477 TYR 0.029 0.001 TYR G1643 ARG 0.008 0.000 ARG F 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7514.47 seconds wall clock time: 132 minutes 8.80 seconds (7928.80 seconds total)