Starting phenix.real_space_refine on Wed Aug 7 06:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/08_2024/8kdc_37131.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/08_2024/8kdc_37131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/08_2024/8kdc_37131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/08_2024/8kdc_37131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/08_2024/8kdc_37131.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/08_2024/8kdc_37131.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 97 5.16 5 C 11999 2.51 5 N 3174 2.21 5 O 3535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2146": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18808 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 17067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2114, 17047 Classifications: {'peptide': 2114} Link IDs: {'PTRANS': 73, 'TRANS': 2040} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 2114, 17047 Classifications: {'peptide': 2114} Link IDs: {'PTRANS': 73, 'TRANS': 2040} Chain breaks: 5 bond proxies already assigned to first conformer: 17372 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: "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 9243 SG CYS A1177 71.681 111.770 64.772 1.00 88.89 S ATOM 9266 SG CYS A1180 73.631 109.989 62.572 1.00 86.70 S ATOM 8907 SG CYS A1132 84.963 107.508 80.610 1.00 82.90 S ATOM 10714 SG CYS A1371 84.136 109.336 76.945 1.00110.51 S ATOM 10720 SG CYS A1372 82.652 106.601 78.646 1.00101.40 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET A 472 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 472 " occ=0.50 residue: pdb=" N ATYR A 649 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 649 " occ=0.50 Time building chain proxies: 18.42, per 1000 atoms: 0.98 Number of scatterers: 18808 At special positions: 0 Unit cell: (115.222, 144.571, 150.006, 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 97 16.00 Mg 1 11.99 O 3535 8.00 N 3174 7.00 C 11999 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: 7.95 Conformation dependent library (CDL) restraints added in 6.7 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 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 11 sheets defined 58.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 48 through 60 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: 3.939A 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: 3.644A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N THR A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 193 Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.557A pdb=" N ASP A 256 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.760A pdb=" N GLN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.711A pdb=" N VAL A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.722A 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 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.850A pdb=" N LYS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.837A 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 471 removed outlier: 3.688A pdb=" N ILE A 470 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 471' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.630A pdb=" N LEU A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.514A pdb=" N VAL A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 527 removed outlier: 4.083A pdb=" N ILE A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.697A pdb=" N THR A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 5.118A 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 763 removed outlier: 4.157A pdb=" N ILE A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.633A pdb=" N LYS A 798 " --> pdb=" O GLU A 794 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 805 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.575A pdb=" N LEU A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) 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 removed outlier: 3.640A pdb=" N LYS A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 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 removed outlier: 3.596A pdb=" N GLU A1041 " --> pdb=" O THR A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 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: 5.187A pdb=" N LYS A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1119 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: 3.974A pdb=" N ARG A1455 " --> pdb=" O SER A1451 " (cutoff:3.500A) removed outlier: 3.909A 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: 5.114A pdb=" N TYR A1499 " --> pdb=" O ASN A1495 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR A1500 " --> pdb=" O GLN A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1523 removed outlier: 4.118A pdb=" N TRP A1513 " --> pdb=" O ARG A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1535 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 Processing helix chain 'A' and resid 1632 through 1651 Processing helix chain 'A' and resid 1670 through 1686 Processing helix chain 'A' and resid 1708 through 1724 removed outlier: 3.716A pdb=" N ASP A1714 " --> pdb=" O LYS A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1769 through 1775 removed outlier: 3.608A pdb=" N GLN A1773 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1774 " --> pdb=" O SER A1771 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1798 removed outlier: 4.435A pdb=" N GLN A1792 " --> pdb=" O LEU A1788 " (cutoff:3.500A) removed outlier: 4.799A 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 1848 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: 3.632A pdb=" N CYS A2181 " --> pdb=" O ASN A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2207 Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.601A pdb=" N HIS B 581 " --> pdb=" O ASN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.605A pdb=" N VAL B 588 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 469 removed outlier: 3.714A pdb=" N ILE C 447 " --> pdb=" O HIS C 443 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 463 Processing helix chain 'E' and resid 435 through 469 Processing helix chain 'F' and resid 435 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.420A pdb=" N THR A 87 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 8.229A 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: 4.812A pdb=" N ILE A 538 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 4.006A 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: 4.137A 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: 4.063A 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: 3.635A pdb=" N LYS A1941 " --> pdb=" O CYS A1904 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASP A1803 " --> pdb=" O ILE A1899 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A1901 " --> pdb=" O ASP A1803 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG A1804 " --> pdb=" O TYR A1828 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN A1830 " --> pdb=" O ARG A1804 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A1806 " --> pdb=" O ASN A1830 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2973 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: 7.82 Time building geometry restraints manager: 8.57 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: 6082 1.34 - 1.46: 2975 1.46 - 1.58: 9942 1.58 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 19159 Sorted by residual: bond pdb=" CB PRO A1993 " pdb=" CG PRO A1993 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO A2068 " pdb=" CG PRO A2068 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.54e+00 bond pdb=" CA GLN A 123 " pdb=" C GLN A 123 " ideal model delta sigma weight residual 1.518 1.572 -0.054 4.01e-02 6.22e+02 1.81e+00 bond pdb=" CB PRO A2144 " pdb=" CG PRO A2144 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.73e+00 bond pdb=" C LEU A1763 " pdb=" N PRO A1764 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 ... (remaining 19154 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.20: 376 106.20 - 113.17: 10563 113.17 - 120.14: 6717 120.14 - 127.12: 8060 127.12 - 134.09: 175 Bond angle restraints: 25891 Sorted by residual: angle pdb=" CA PRO A1993 " pdb=" N PRO A1993 " pdb=" CD PRO A1993 " ideal model delta sigma weight residual 112.00 107.53 4.47 1.40e+00 5.10e-01 1.02e+01 angle pdb=" CA PRO A2068 " pdb=" N PRO A2068 " pdb=" CD PRO A2068 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.64e+00 angle pdb=" CA PRO A2144 " pdb=" N PRO A2144 " pdb=" CD PRO A2144 " ideal model delta sigma weight residual 112.00 107.82 4.18 1.40e+00 5.10e-01 8.90e+00 angle pdb=" CA MET A1517 " pdb=" CB MET A1517 " pdb=" CG MET A1517 " ideal model delta sigma weight residual 114.10 108.53 5.57 2.00e+00 2.50e-01 7.76e+00 angle pdb=" N ASP A 651 " pdb=" CA ASP A 651 " pdb=" C ASP A 651 " ideal model delta sigma weight residual 113.28 108.92 4.36 1.57e+00 4.06e-01 7.71e+00 ... (remaining 25886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10459 17.90 - 35.79: 1018 35.79 - 53.69: 166 53.69 - 71.58: 30 71.58 - 89.48: 9 Dihedral angle restraints: 11682 sinusoidal: 4815 harmonic: 6867 Sorted by residual: dihedral pdb=" CA TYR A 42 " pdb=" C TYR A 42 " pdb=" N ASP A 43 " pdb=" CA ASP A 43 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 535 " pdb=" CG GLU A 535 " pdb=" CD GLU A 535 " pdb=" OE1 GLU A 535 " ideal model delta sinusoidal sigma weight residual 0.00 -89.48 89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 126 " pdb=" CB ASP A 126 " pdb=" CG ASP A 126 " pdb=" OD1 ASP A 126 " ideal model delta sinusoidal sigma weight residual -30.00 -85.53 55.53 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 11679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2319 0.046 - 0.092: 522 0.092 - 0.138: 100 0.138 - 0.185: 5 0.185 - 0.231: 1 Chirality restraints: 2947 Sorted by residual: chirality pdb=" CB ILE A1307 " pdb=" CA ILE A1307 " pdb=" CG1 ILE A1307 " pdb=" CG2 ILE A1307 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 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 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CB VAL A1798 " pdb=" CA VAL A1798 " pdb=" CG1 VAL A1798 " pdb=" CG2 VAL A1798 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 2944 not shown) Planarity restraints: 3270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2067 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A2068 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A2068 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A2068 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1992 " 0.067 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO A1993 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A1993 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1993 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A2143 " -0.040 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A2144 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A2144 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2144 " -0.032 5.00e-02 4.00e+02 ... (remaining 3267 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 115 2.58 - 3.16: 15273 3.16 - 3.74: 28142 3.74 - 4.32: 37550 4.32 - 4.90: 66755 Nonbonded interactions: 147835 Sorted by model distance: nonbonded pdb=" OE2 GLU A1164 " pdb="ZN ZN A3003 " model vdw 2.001 2.230 nonbonded pdb=" OD2 ASP A 773 " pdb="MG MG A3001 " model vdw 2.068 2.170 nonbonded pdb=" OE1 GLU A2033 " pdb=" NH2 ARG A2042 " model vdw 2.165 3.120 nonbonded pdb=" O SER A 857 " pdb=" ND2 ASN A 870 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASN B 542 " pdb=" OG1 THR B 544 " model vdw 2.240 3.040 ... (remaining 147830 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' 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: 2.340 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: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 68.930 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 0.083 19159 Z= 0.179 Angle : 0.495 6.522 25891 Z= 0.263 Chirality : 0.039 0.231 2947 Planarity : 0.004 0.108 3270 Dihedral : 14.094 89.480 7234 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.18), residues: 2313 helix: 2.11 (0.15), residues: 1286 sheet: -0.14 (0.40), residues: 177 loop : -1.16 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A2188 HIS 0.007 0.001 HIS A2059 PHE 0.020 0.001 PHE A 99 TYR 0.027 0.001 TYR A 164 ARG 0.003 0.000 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.893 Fit side-chains REVERT: A 523 ASP cc_start: 0.8092 (t0) cc_final: 0.7854 (t70) REVERT: A 1398 GLU cc_start: 0.8458 (pt0) cc_final: 0.8209 (pm20) REVERT: A 1770 LEU cc_start: 0.8442 (mp) cc_final: 0.7738 (tp) REVERT: A 1906 MET cc_start: 0.7701 (mtm) cc_final: 0.5414 (mtm) REVERT: A 1920 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7195 (tt0) REVERT: A 2063 GLU cc_start: 0.7235 (mt-10) cc_final: 0.7025 (mt-10) REVERT: C 465 LYS cc_start: 0.7599 (ttmm) cc_final: 0.7195 (ttmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3285 time to fit residues: 133.4154 Evaluate side-chains 212 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 GLN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19159 Z= 0.323 Angle : 0.566 7.334 25891 Z= 0.296 Chirality : 0.042 0.186 2947 Planarity : 0.004 0.082 3270 Dihedral : 4.064 18.288 2531 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.85 % Allowed : 6.44 % Favored : 92.71 % 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: 1.04 (0.18), residues: 2313 helix: 2.02 (0.15), residues: 1290 sheet: -0.20 (0.40), residues: 177 loop : -1.26 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1880 HIS 0.004 0.001 HIS A2059 PHE 0.019 0.002 PHE A 99 TYR 0.016 0.002 TYR A2044 ARG 0.004 0.000 ARG A2082 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 222 time to evaluate : 2.219 Fit side-chains REVERT: A 523 ASP cc_start: 0.8288 (t0) cc_final: 0.7836 (t0) REVERT: A 1368 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 1415 MET cc_start: 0.7639 (mmt) cc_final: 0.7415 (mmm) REVERT: A 1514 ASP cc_start: 0.7810 (t70) cc_final: 0.7424 (t0) REVERT: A 1770 LEU cc_start: 0.8498 (mp) cc_final: 0.7795 (tp) REVERT: A 1795 MET cc_start: 0.8133 (ptm) cc_final: 0.7602 (ptm) REVERT: A 1875 ASN cc_start: 0.8649 (t0) cc_final: 0.8303 (t0) REVERT: A 1906 MET cc_start: 0.7726 (mtm) cc_final: 0.5732 (mtm) REVERT: A 1920 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7270 (tt0) REVERT: A 2198 MET cc_start: 0.7637 (mmm) cc_final: 0.7326 (mmm) REVERT: C 465 LYS cc_start: 0.7585 (ttmm) cc_final: 0.7177 (ttmm) outliers start: 17 outliers final: 9 residues processed: 234 average time/residue: 0.3385 time to fit residues: 120.8007 Evaluate side-chains 217 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain E residue 468 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 HIS ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19159 Z= 0.220 Angle : 0.513 8.187 25891 Z= 0.268 Chirality : 0.040 0.160 2947 Planarity : 0.004 0.071 3270 Dihedral : 3.984 18.728 2531 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.03 % Allowed : 7.95 % Favored : 91.02 % 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: 1.15 (0.18), residues: 2313 helix: 2.15 (0.15), residues: 1284 sheet: -0.23 (0.40), residues: 177 loop : -1.23 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2188 HIS 0.004 0.001 HIS A2059 PHE 0.018 0.001 PHE A1578 TYR 0.012 0.001 TYR A 942 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 2.244 Fit side-chains revert: symmetry clash REVERT: A 466 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7252 (mt-10) REVERT: A 523 ASP cc_start: 0.8255 (t0) cc_final: 0.7732 (t0) REVERT: A 1368 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 1415 MET cc_start: 0.7618 (mmt) cc_final: 0.7380 (mmm) REVERT: A 1514 ASP cc_start: 0.7795 (t70) cc_final: 0.7410 (t0) REVERT: A 1770 LEU cc_start: 0.8461 (mp) cc_final: 0.7759 (tp) REVERT: A 1795 MET cc_start: 0.8051 (ptm) cc_final: 0.7548 (ptm) REVERT: A 1875 ASN cc_start: 0.8616 (t0) cc_final: 0.8267 (t0) REVERT: A 1906 MET cc_start: 0.7687 (mtm) cc_final: 0.5863 (mtm) REVERT: A 1920 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7235 (tt0) REVERT: A 2188 TRP cc_start: 0.8076 (m100) cc_final: 0.7609 (m100) REVERT: A 2198 MET cc_start: 0.7686 (mmm) cc_final: 0.7434 (mmm) outliers start: 21 outliers final: 14 residues processed: 232 average time/residue: 0.3238 time to fit residues: 114.5259 Evaluate side-chains 218 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 140 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19159 Z= 0.211 Angle : 0.500 7.969 25891 Z= 0.261 Chirality : 0.040 0.188 2947 Planarity : 0.004 0.066 3270 Dihedral : 3.929 20.939 2531 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.03 % Allowed : 9.17 % Favored : 89.79 % 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: 1.19 (0.18), residues: 2313 helix: 2.19 (0.15), residues: 1284 sheet: -0.20 (0.40), residues: 177 loop : -1.24 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1880 HIS 0.002 0.001 HIS A1921 PHE 0.018 0.001 PHE A1578 TYR 0.013 0.001 TYR A 607 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 2.331 Fit side-chains revert: symmetry clash REVERT: A 466 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7281 (mt-10) REVERT: A 523 ASP cc_start: 0.8255 (t0) cc_final: 0.7712 (t0) REVERT: A 651 ASP cc_start: 0.8014 (t0) cc_final: 0.7800 (t0) REVERT: A 689 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7527 (pp) REVERT: A 1368 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7572 (mm-30) REVERT: A 1415 MET cc_start: 0.7621 (mmt) cc_final: 0.7379 (mmm) REVERT: A 1514 ASP cc_start: 0.7780 (t70) cc_final: 0.7396 (t0) REVERT: A 1770 LEU cc_start: 0.8463 (mp) cc_final: 0.7747 (tp) REVERT: A 1795 MET cc_start: 0.8051 (ptm) cc_final: 0.7634 (ptm) REVERT: A 1875 ASN cc_start: 0.8628 (t0) cc_final: 0.8237 (t0) REVERT: A 1906 MET cc_start: 0.7666 (mtm) cc_final: 0.5923 (mtm) REVERT: A 1920 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7235 (tt0) REVERT: A 2033 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 2188 TRP cc_start: 0.8141 (m100) cc_final: 0.7737 (m100) REVERT: B 577 ASN cc_start: 0.7887 (m110) cc_final: 0.7600 (m-40) outliers start: 21 outliers final: 15 residues processed: 228 average time/residue: 0.3373 time to fit residues: 117.4426 Evaluate side-chains 225 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 209 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 91 optimal weight: 0.0470 chunk 189 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 0.0020 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19159 Z= 0.236 Angle : 0.507 7.579 25891 Z= 0.265 Chirality : 0.040 0.163 2947 Planarity : 0.004 0.061 3270 Dihedral : 3.926 18.942 2531 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.22 % Allowed : 9.74 % Favored : 89.04 % 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: 1.17 (0.18), residues: 2313 helix: 2.19 (0.15), residues: 1284 sheet: -0.19 (0.40), residues: 177 loop : -1.27 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1880 HIS 0.012 0.001 HIS A2059 PHE 0.017 0.002 PHE A1578 TYR 0.021 0.001 TYR A1422 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 2.200 Fit side-chains revert: symmetry clash REVERT: A 466 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7382 (mt-10) REVERT: A 523 ASP cc_start: 0.8306 (t0) cc_final: 0.7789 (t0) REVERT: A 689 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7585 (pp) REVERT: A 1368 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 1415 MET cc_start: 0.7638 (mmt) cc_final: 0.7384 (mmm) REVERT: A 1514 ASP cc_start: 0.7790 (t70) cc_final: 0.7405 (t0) REVERT: A 1770 LEU cc_start: 0.8473 (mp) cc_final: 0.7766 (tp) REVERT: A 1795 MET cc_start: 0.8029 (ptm) cc_final: 0.7614 (ptm) REVERT: A 1875 ASN cc_start: 0.8655 (t0) cc_final: 0.8224 (t0) REVERT: A 1906 MET cc_start: 0.7685 (mtm) cc_final: 0.5904 (mtm) REVERT: A 1920 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7232 (tt0) REVERT: A 2188 TRP cc_start: 0.8246 (m100) cc_final: 0.7749 (m100) REVERT: B 577 ASN cc_start: 0.7820 (m110) cc_final: 0.7488 (m110) outliers start: 25 outliers final: 18 residues processed: 237 average time/residue: 0.3262 time to fit residues: 117.1290 Evaluate side-chains 232 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain E residue 462 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 0.0030 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19159 Z= 0.145 Angle : 0.466 7.247 25891 Z= 0.244 Chirality : 0.038 0.152 2947 Planarity : 0.003 0.057 3270 Dihedral : 3.739 18.139 2531 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.89 % Allowed : 10.63 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.18), residues: 2313 helix: 2.39 (0.15), residues: 1285 sheet: -0.12 (0.40), residues: 177 loop : -1.23 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1880 HIS 0.010 0.001 HIS A2059 PHE 0.019 0.001 PHE A1578 TYR 0.013 0.001 TYR A 607 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8203 (t0) cc_final: 0.7660 (t0) REVERT: A 689 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7294 (pp) REVERT: A 819 LYS cc_start: 0.7379 (ptpt) cc_final: 0.7077 (pttp) REVERT: A 997 ASP cc_start: 0.8080 (t70) cc_final: 0.7798 (t70) REVERT: A 1368 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 1398 GLU cc_start: 0.8532 (pt0) cc_final: 0.8325 (pm20) REVERT: A 1415 MET cc_start: 0.7611 (mmt) cc_final: 0.7349 (mmm) REVERT: A 1514 ASP cc_start: 0.7740 (t70) cc_final: 0.7359 (t0) REVERT: A 1770 LEU cc_start: 0.8400 (mp) cc_final: 0.7685 (tp) REVERT: A 1795 MET cc_start: 0.7895 (ptm) cc_final: 0.7541 (ptm) REVERT: A 1875 ASN cc_start: 0.8600 (t0) cc_final: 0.8070 (t0) REVERT: A 1906 MET cc_start: 0.7650 (mtm) cc_final: 0.5901 (mtm) REVERT: A 1920 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7218 (tt0) REVERT: A 2188 TRP cc_start: 0.8197 (m100) cc_final: 0.7728 (m100) REVERT: A 2198 MET cc_start: 0.7610 (mmm) cc_final: 0.7262 (mmm) REVERT: B 577 ASN cc_start: 0.7935 (m110) cc_final: 0.7617 (m110) outliers start: 18 outliers final: 12 residues processed: 237 average time/residue: 0.3260 time to fit residues: 118.2505 Evaluate side-chains 224 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain E residue 462 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 19159 Z= 0.203 Angle : 0.490 7.404 25891 Z= 0.257 Chirality : 0.039 0.153 2947 Planarity : 0.004 0.056 3270 Dihedral : 3.756 17.780 2531 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.85 % Allowed : 11.05 % Favored : 88.10 % 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: 1.37 (0.18), residues: 2313 helix: 2.36 (0.15), residues: 1285 sheet: -0.10 (0.40), residues: 177 loop : -1.23 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1880 HIS 0.010 0.001 HIS A2059 PHE 0.017 0.001 PHE A1578 TYR 0.022 0.001 TYR A1422 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 2.260 Fit side-chains revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8211 (t0) cc_final: 0.7667 (t0) REVERT: A 689 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7456 (pp) REVERT: A 819 LYS cc_start: 0.7388 (ptpt) cc_final: 0.7094 (pttp) REVERT: A 1368 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1398 GLU cc_start: 0.8567 (pt0) cc_final: 0.8292 (pm20) REVERT: A 1415 MET cc_start: 0.7631 (mmt) cc_final: 0.7371 (mmm) REVERT: A 1514 ASP cc_start: 0.7757 (t70) cc_final: 0.7378 (t0) REVERT: A 1770 LEU cc_start: 0.8349 (mp) cc_final: 0.7644 (tp) REVERT: A 1795 MET cc_start: 0.7920 (ptm) cc_final: 0.7549 (ptm) REVERT: A 1875 ASN cc_start: 0.8620 (t0) cc_final: 0.8239 (t0) REVERT: A 1906 MET cc_start: 0.7657 (mtm) cc_final: 0.5874 (mtm) REVERT: A 1920 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7202 (tt0) REVERT: A 2188 TRP cc_start: 0.8268 (m100) cc_final: 0.7640 (m100) REVERT: A 2198 MET cc_start: 0.7650 (mmm) cc_final: 0.7321 (mmm) REVERT: B 577 ASN cc_start: 0.7934 (m110) cc_final: 0.7614 (m110) REVERT: D 469 GLU cc_start: 0.8482 (pm20) cc_final: 0.8226 (pm20) outliers start: 17 outliers final: 12 residues processed: 225 average time/residue: 0.3680 time to fit residues: 125.9050 Evaluate side-chains 227 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 19159 Z= 0.245 Angle : 0.514 7.552 25891 Z= 0.270 Chirality : 0.040 0.158 2947 Planarity : 0.004 0.056 3270 Dihedral : 3.853 18.307 2531 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.89 % Allowed : 11.24 % Favored : 87.86 % 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: 1.27 (0.18), residues: 2313 helix: 2.28 (0.15), residues: 1285 sheet: -0.14 (0.40), residues: 177 loop : -1.25 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1880 HIS 0.004 0.001 HIS A2059 PHE 0.016 0.002 PHE A1578 TYR 0.014 0.001 TYR A 942 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.235 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.8518 (mtp) cc_final: 0.8062 (mtp) REVERT: A 523 ASP cc_start: 0.8239 (t0) cc_final: 0.7708 (t0) REVERT: A 689 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7575 (pp) REVERT: A 819 LYS cc_start: 0.7440 (ptpt) cc_final: 0.7099 (pttp) REVERT: A 997 ASP cc_start: 0.8106 (t70) cc_final: 0.7814 (t70) REVERT: A 1368 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 1415 MET cc_start: 0.7658 (mmt) cc_final: 0.7390 (mmm) REVERT: A 1514 ASP cc_start: 0.7790 (t70) cc_final: 0.7413 (t0) REVERT: A 1770 LEU cc_start: 0.8360 (mp) cc_final: 0.7661 (tp) REVERT: A 1795 MET cc_start: 0.8002 (ptm) cc_final: 0.7604 (ptm) REVERT: A 1875 ASN cc_start: 0.8604 (t0) cc_final: 0.8236 (t0) REVERT: A 1906 MET cc_start: 0.7638 (mtm) cc_final: 0.5875 (mtm) REVERT: A 1920 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7203 (tt0) REVERT: A 2188 TRP cc_start: 0.8264 (m100) cc_final: 0.7720 (m100) REVERT: A 2198 MET cc_start: 0.7660 (mmm) cc_final: 0.7315 (mmm) REVERT: B 577 ASN cc_start: 0.7958 (m110) cc_final: 0.7619 (m110) REVERT: B 598 ASP cc_start: 0.7484 (m-30) cc_final: 0.7283 (m-30) REVERT: D 469 GLU cc_start: 0.8543 (pm20) cc_final: 0.8283 (pm20) outliers start: 18 outliers final: 15 residues processed: 227 average time/residue: 0.3273 time to fit residues: 112.7572 Evaluate side-chains 227 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 19159 Z= 0.273 Angle : 0.535 7.710 25891 Z= 0.280 Chirality : 0.040 0.157 2947 Planarity : 0.004 0.055 3270 Dihedral : 3.919 18.575 2531 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.80 % Allowed : 11.57 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.18), residues: 2313 helix: 2.19 (0.15), residues: 1285 sheet: -0.21 (0.40), residues: 177 loop : -1.28 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1880 HIS 0.011 0.001 HIS A2059 PHE 0.016 0.002 PHE A 400 TYR 0.023 0.001 TYR A1422 ARG 0.006 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 209 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.8487 (mtp) cc_final: 0.8065 (mtp) REVERT: A 523 ASP cc_start: 0.8272 (t0) cc_final: 0.7975 (t0) REVERT: A 689 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7608 (pp) REVERT: A 819 LYS cc_start: 0.7401 (ptpt) cc_final: 0.7066 (pttp) REVERT: A 1368 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 1415 MET cc_start: 0.7671 (mmt) cc_final: 0.7400 (mmm) REVERT: A 1514 ASP cc_start: 0.7786 (t70) cc_final: 0.7408 (t0) REVERT: A 1770 LEU cc_start: 0.8393 (mp) cc_final: 0.7664 (tp) REVERT: A 1795 MET cc_start: 0.8080 (ptm) cc_final: 0.7659 (ptm) REVERT: A 1875 ASN cc_start: 0.8644 (t0) cc_final: 0.8403 (t0) REVERT: A 2188 TRP cc_start: 0.8289 (m100) cc_final: 0.7728 (m100) REVERT: A 2198 MET cc_start: 0.7679 (mmm) cc_final: 0.7334 (mmm) REVERT: B 577 ASN cc_start: 0.7956 (m110) cc_final: 0.7603 (m110) REVERT: D 469 GLU cc_start: 0.8533 (pm20) cc_final: 0.8277 (pm20) outliers start: 16 outliers final: 15 residues processed: 221 average time/residue: 0.3304 time to fit residues: 110.8795 Evaluate side-chains 224 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 151 optimal weight: 0.0670 chunk 229 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 19159 Z= 0.193 Angle : 0.499 7.480 25891 Z= 0.262 Chirality : 0.039 0.152 2947 Planarity : 0.004 0.055 3270 Dihedral : 3.799 18.125 2531 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.85 % Allowed : 11.52 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.18), residues: 2313 helix: 2.32 (0.15), residues: 1284 sheet: -0.21 (0.39), residues: 177 loop : -1.24 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1880 HIS 0.008 0.001 HIS A2059 PHE 0.018 0.001 PHE A1578 TYR 0.014 0.001 TYR A 607 ARG 0.006 0.000 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8229 (t0) cc_final: 0.7697 (t0) REVERT: A 689 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7509 (pp) REVERT: A 819 LYS cc_start: 0.7297 (ptpt) cc_final: 0.7065 (pttp) REVERT: A 997 ASP cc_start: 0.8091 (t70) cc_final: 0.7812 (t70) REVERT: A 1368 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 1398 GLU cc_start: 0.8546 (pt0) cc_final: 0.8308 (pm20) REVERT: A 1415 MET cc_start: 0.7582 (mmt) cc_final: 0.7327 (mmm) REVERT: A 1514 ASP cc_start: 0.7743 (t70) cc_final: 0.7365 (t0) REVERT: A 1770 LEU cc_start: 0.8330 (mp) cc_final: 0.7628 (tp) REVERT: A 1795 MET cc_start: 0.8006 (ptm) cc_final: 0.7614 (ptm) REVERT: A 1962 LYS cc_start: 0.7413 (pptt) cc_final: 0.6974 (ptpp) REVERT: A 2188 TRP cc_start: 0.8275 (m100) cc_final: 0.7752 (m100) REVERT: A 2198 MET cc_start: 0.7684 (mmm) cc_final: 0.7291 (mmm) REVERT: B 577 ASN cc_start: 0.7780 (m110) cc_final: 0.7414 (m110) REVERT: D 469 GLU cc_start: 0.8504 (pm20) cc_final: 0.8267 (pm20) outliers start: 17 outliers final: 15 residues processed: 222 average time/residue: 0.3377 time to fit residues: 114.4651 Evaluate side-chains 224 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 187 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104219 restraints weight = 50363.106| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.72 r_work: 0.3168 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 19159 Z= 0.178 Angle : 0.492 7.371 25891 Z= 0.258 Chirality : 0.039 0.159 2947 Planarity : 0.003 0.055 3270 Dihedral : 3.736 17.575 2531 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.94 % Allowed : 11.71 % Favored : 87.35 % 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: 1.37 (0.18), residues: 2313 helix: 2.37 (0.15), residues: 1285 sheet: -0.16 (0.40), residues: 177 loop : -1.23 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1880 HIS 0.005 0.001 HIS A2059 PHE 0.018 0.001 PHE A1578 TYR 0.023 0.001 TYR A1422 ARG 0.006 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3934.29 seconds wall clock time: 71 minutes 7.64 seconds (4267.64 seconds total)