Starting phenix.real_space_refine on Mon Jul 22 16:15:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/07_2024/8kdc_37131_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/07_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_37131/07_2024/8kdc_37131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/07_2024/8kdc_37131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/07_2024/8kdc_37131_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdc_37131/07_2024/8kdc_37131_neut.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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 17.21, per 1000 atoms: 0.92 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: 7.22 Conformation dependent library (CDL) restraints added in 5.7 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: 2.39 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: 7.95 Time building geometry restraints manager: 7.78 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 2.520 nonbonded pdb=" O SER A 857 " pdb=" ND2 ASN A 870 " model vdw 2.206 2.520 nonbonded pdb=" OD1 ASN B 542 " pdb=" OG1 THR B 544 " model vdw 2.240 2.440 ... (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 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 65.130 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.230 ------------------------------------------------------------------------------- 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 : 1.880 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: 0.3185 time to fit residues: 128.4361 Evaluate side-chains 212 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.0828 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= 0.306 Angle : 0.551 7.312 25891 Z= 0.287 Chirality : 0.041 0.173 2947 Planarity : 0.004 0.079 3270 Dihedral : 4.013 17.139 2531 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.03 % Allowed : 6.21 % Favored : 92.76 % 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: 1.08 (0.18), residues: 2313 helix: 2.08 (0.15), residues: 1284 sheet: -0.11 (0.40), residues: 176 loop : -1.28 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2188 HIS 0.005 0.001 HIS A2059 PHE 0.020 0.002 PHE A 99 TYR 0.015 0.002 TYR A2044 ARG 0.003 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 243 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8248 (t0) cc_final: 0.7767 (t0) REVERT: A 1415 MET cc_start: 0.7624 (mmt) cc_final: 0.7400 (mmm) REVERT: A 1514 ASP cc_start: 0.7825 (t70) cc_final: 0.7440 (t0) REVERT: A 1770 LEU cc_start: 0.8506 (mp) cc_final: 0.7805 (tp) REVERT: A 1795 MET cc_start: 0.8118 (ptm) cc_final: 0.7588 (ptm) REVERT: A 1906 MET cc_start: 0.7670 (mtm) cc_final: 0.5625 (mtm) REVERT: A 1920 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7280 (tt0) REVERT: A 2198 MET cc_start: 0.7555 (mmm) cc_final: 0.7284 (mmm) REVERT: C 465 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7221 (ttmm) outliers start: 21 outliers final: 13 residues processed: 234 average time/residue: 0.3282 time to fit residues: 116.5192 Evaluate side-chains 224 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1184 ASP Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 2083 THR Chi-restraints excluded: chain A residue 2164 LEU 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: 3.9990 chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0851 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= 0.202 Angle : 0.493 7.220 25891 Z= 0.257 Chirality : 0.039 0.157 2947 Planarity : 0.004 0.068 3270 Dihedral : 3.911 17.088 2531 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.80 % Allowed : 8.65 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2313 helix: 2.24 (0.15), residues: 1283 sheet: -0.14 (0.40), residues: 176 loop : -1.23 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2188 HIS 0.005 0.001 HIS A2059 PHE 0.018 0.001 PHE A1578 TYR 0.013 0.001 TYR A 607 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 235 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.117 Fit side-chains REVERT: A 344 ASP cc_start: 0.8296 (m-30) cc_final: 0.8080 (m-30) REVERT: A 523 ASP cc_start: 0.8243 (t0) cc_final: 0.7743 (t0) REVERT: A 1398 GLU cc_start: 0.8515 (pt0) cc_final: 0.8301 (pm20) REVERT: A 1415 MET cc_start: 0.7599 (mmt) cc_final: 0.7360 (mmm) REVERT: A 1514 ASP cc_start: 0.7787 (t70) cc_final: 0.7400 (t0) REVERT: A 1770 LEU cc_start: 0.8461 (mp) cc_final: 0.7766 (tp) REVERT: A 1795 MET cc_start: 0.8021 (ptm) cc_final: 0.7505 (ptm) REVERT: A 1906 MET cc_start: 0.7666 (mtm) cc_final: 0.5840 (mtm) REVERT: A 1920 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7203 (tt0) REVERT: A 2198 MET cc_start: 0.7643 (mmm) cc_final: 0.7428 (mmm) REVERT: B 577 ASN cc_start: 0.7927 (m110) cc_final: 0.7632 (m-40) outliers start: 16 outliers final: 12 residues processed: 231 average time/residue: 0.3218 time to fit residues: 113.2526 Evaluate side-chains 221 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 2.064 ------------------------------------------------------------------------------- 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 521 ILE Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2164 LEU 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: 7.9990 chunk 157 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN A1147 HIS ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1079 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= 0.288 Angle : 0.533 8.285 25891 Z= 0.277 Chirality : 0.041 0.193 2947 Planarity : 0.004 0.063 3270 Dihedral : 4.016 20.395 2531 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.46 % Allowed : 9.41 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.18), residues: 2313 helix: 2.13 (0.15), residues: 1283 sheet: -0.18 (0.40), residues: 176 loop : -1.32 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A2188 HIS 0.003 0.001 HIS A1364 PHE 0.017 0.002 PHE A 358 TYR 0.014 0.001 TYR A2044 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 243 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 2.093 Fit side-chains REVERT: A 344 ASP cc_start: 0.8323 (m-30) cc_final: 0.8117 (m-30) REVERT: A 523 ASP cc_start: 0.8284 (t0) cc_final: 0.7970 (t0) REVERT: A 651 ASP cc_start: 0.8052 (t0) cc_final: 0.7844 (t0) REVERT: A 689 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7632 (pp) REVERT: A 1368 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 1415 MET cc_start: 0.7631 (mmt) cc_final: 0.7379 (mmm) REVERT: A 1514 ASP cc_start: 0.7796 (t70) cc_final: 0.7405 (t0) REVERT: A 1770 LEU cc_start: 0.8498 (mp) cc_final: 0.7794 (tp) REVERT: A 1795 MET cc_start: 0.8083 (ptm) cc_final: 0.7634 (ptm) REVERT: A 1906 MET cc_start: 0.7692 (mtm) cc_final: 0.5853 (mtm) REVERT: A 1920 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7247 (tt0) REVERT: A 2188 TRP cc_start: 0.8143 (m100) cc_final: 0.7744 (m100) REVERT: A 2198 MET cc_start: 0.7755 (mmm) cc_final: 0.7488 (mmm) REVERT: B 577 ASN cc_start: 0.7862 (m110) cc_final: 0.7540 (m110) outliers start: 30 outliers final: 23 residues processed: 232 average time/residue: 0.3681 time to fit residues: 131.0720 Evaluate side-chains 236 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 2.550 ------------------------------------------------------------------------------- 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 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 1096 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1184 ASP 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 1782 THR Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 468 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 113 optimal weight: 0.0470 chunk 199 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN ** 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: 0.7694 moved from start: 0.1117 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= 0.255 Angle : 0.513 8.190 25891 Z= 0.267 Chirality : 0.040 0.184 2947 Planarity : 0.004 0.059 3270 Dihedral : 3.982 23.575 2531 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 9.83 % Favored : 88.66 % 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: 1.14 (0.18), residues: 2313 helix: 2.19 (0.15), residues: 1282 sheet: -0.23 (0.40), residues: 176 loop : -1.32 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2188 HIS 0.005 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 246 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 2.083 Fit side-chains REVERT: A 344 ASP cc_start: 0.8324 (m-30) cc_final: 0.8103 (m-30) REVERT: A 523 ASP cc_start: 0.8235 (t0) cc_final: 0.7902 (t0) REVERT: A 689 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7609 (pp) REVERT: A 1368 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1415 MET cc_start: 0.7641 (mmt) cc_final: 0.7382 (mmm) REVERT: A 1514 ASP cc_start: 0.7795 (t70) cc_final: 0.7405 (t0) REVERT: A 1770 LEU cc_start: 0.8461 (mp) cc_final: 0.7737 (tp) REVERT: A 1795 MET cc_start: 0.8046 (ptm) cc_final: 0.7610 (ptm) REVERT: A 1906 MET cc_start: 0.7674 (mtm) cc_final: 0.5857 (mtm) REVERT: A 1920 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7237 (tt0) REVERT: A 2188 TRP cc_start: 0.8208 (m100) cc_final: 0.7823 (m100) REVERT: A 2198 MET cc_start: 0.7692 (mmm) cc_final: 0.7382 (mmm) REVERT: B 577 ASN cc_start: 0.7796 (m110) cc_final: 0.7426 (m110) outliers start: 31 outliers final: 27 residues processed: 234 average time/residue: 0.3245 time to fit residues: 115.5580 Evaluate side-chains 236 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 440 SER 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 1096 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1184 ASP 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 1782 THR 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 1928 THR Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2083 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 585 ASP 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: 0.4980 chunk 200 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 222 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1773 GLN ** A1875 ASN ** 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: 0.7662 moved from start: 0.1092 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= 0.178 Angle : 0.478 7.784 25891 Z= 0.249 Chirality : 0.039 0.155 2947 Planarity : 0.003 0.056 3270 Dihedral : 3.829 18.099 2531 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.99 % Allowed : 11.15 % 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: 1.33 (0.18), residues: 2313 helix: 2.37 (0.15), residues: 1283 sheet: -0.18 (0.40), residues: 176 loop : -1.28 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1880 HIS 0.003 0.001 HIS A2059 PHE 0.019 0.001 PHE A1578 TYR 0.031 0.001 TYR A 942 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 239 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 2.326 Fit side-chains REVERT: A 344 ASP cc_start: 0.8299 (m-30) cc_final: 0.8089 (m-30) REVERT: A 523 ASP cc_start: 0.8181 (t0) cc_final: 0.7640 (t0) REVERT: A 689 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7414 (pp) REVERT: A 819 LYS cc_start: 0.7425 (ptpt) cc_final: 0.7099 (mtmm) REVERT: A 1368 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 1415 MET cc_start: 0.7618 (mmt) cc_final: 0.7367 (mmm) REVERT: A 1514 ASP cc_start: 0.7763 (t70) cc_final: 0.7385 (t0) REVERT: A 1770 LEU cc_start: 0.8378 (mp) cc_final: 0.7631 (tp) REVERT: A 1795 MET cc_start: 0.8031 (ptm) cc_final: 0.7601 (ptm) REVERT: A 1906 MET cc_start: 0.7640 (mtm) cc_final: 0.5836 (mtm) REVERT: A 1920 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7189 (tt0) REVERT: A 2188 TRP cc_start: 0.8238 (m100) cc_final: 0.7783 (m100) REVERT: B 577 ASN cc_start: 0.7926 (m110) cc_final: 0.7594 (m110) outliers start: 20 outliers final: 16 residues processed: 233 average time/residue: 0.3214 time to fit residues: 114.1297 Evaluate side-chains 225 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN 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 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1096 THR 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 1928 THR Chi-restraints excluded: chain A residue 2083 THR 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: 1.9990 chunk 126 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 187 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS E 443 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 19159 Z= 0.217 Angle : 0.492 7.570 25891 Z= 0.257 Chirality : 0.039 0.155 2947 Planarity : 0.004 0.054 3270 Dihedral : 3.817 17.186 2531 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.32 % Allowed : 11.43 % Favored : 87.25 % 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: 2.35 (0.15), residues: 1283 sheet: -0.17 (0.40), residues: 176 loop : -1.29 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1880 HIS 0.005 0.001 HIS A2059 PHE 0.018 0.001 PHE A1578 TYR 0.021 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 240 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 2.094 Fit side-chains REVERT: A 344 ASP cc_start: 0.8321 (m-30) cc_final: 0.8093 (m-30) REVERT: A 523 ASP cc_start: 0.8175 (t0) cc_final: 0.7635 (t0) REVERT: A 689 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7481 (pp) REVERT: A 819 LYS cc_start: 0.7407 (ptpt) cc_final: 0.7085 (pttp) REVERT: A 1368 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 1415 MET cc_start: 0.7607 (mmt) cc_final: 0.7342 (mmm) REVERT: A 1514 ASP cc_start: 0.7793 (t70) cc_final: 0.7417 (t0) REVERT: A 1770 LEU cc_start: 0.8444 (mp) cc_final: 0.7713 (tp) REVERT: A 1795 MET cc_start: 0.8033 (ptm) cc_final: 0.7606 (ptm) REVERT: A 1906 MET cc_start: 0.7642 (mtm) cc_final: 0.5798 (mtm) REVERT: A 1920 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7195 (tt0) REVERT: A 2188 TRP cc_start: 0.8236 (m100) cc_final: 0.7688 (m100) REVERT: B 577 ASN cc_start: 0.7867 (m110) cc_final: 0.7507 (m110) outliers start: 27 outliers final: 22 residues processed: 229 average time/residue: 0.3240 time to fit residues: 112.8471 Evaluate side-chains 232 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 440 SER 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 1096 THR 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 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2083 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 585 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19159 Z= 0.297 Angle : 0.531 7.635 25891 Z= 0.277 Chirality : 0.041 0.166 2947 Planarity : 0.004 0.053 3270 Dihedral : 3.944 17.467 2531 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.46 % Allowed : 11.34 % Favored : 87.21 % 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: 1.15 (0.18), residues: 2313 helix: 2.20 (0.15), residues: 1285 sheet: -0.23 (0.40), residues: 176 loop : -1.35 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1880 HIS 0.005 0.001 HIS A2059 PHE 0.017 0.002 PHE A 400 TYR 0.015 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 238 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: A 344 ASP cc_start: 0.8339 (m-30) cc_final: 0.8115 (m-30) REVERT: A 523 ASP cc_start: 0.8232 (t0) cc_final: 0.7923 (t0) REVERT: A 689 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7617 (pp) REVERT: A 819 LYS cc_start: 0.7436 (ptpt) cc_final: 0.7078 (pttp) REVERT: A 1514 ASP cc_start: 0.7804 (t70) cc_final: 0.7423 (t0) REVERT: A 1770 LEU cc_start: 0.8430 (mp) cc_final: 0.7697 (tp) REVERT: A 1795 MET cc_start: 0.8082 (ptm) cc_final: 0.7627 (ptm) REVERT: A 2188 TRP cc_start: 0.8236 (m100) cc_final: 0.7477 (m100) REVERT: B 577 ASN cc_start: 0.7814 (m110) cc_final: 0.7433 (m110) REVERT: C 465 LYS cc_start: 0.7440 (ttmt) cc_final: 0.7017 (ttmm) outliers start: 30 outliers final: 26 residues processed: 229 average time/residue: 0.3454 time to fit residues: 119.5764 Evaluate side-chains 234 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 206 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 320 MET 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 1096 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1184 ASP 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 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2083 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 585 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 124 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19159 Z= 0.202 Angle : 0.493 7.432 25891 Z= 0.257 Chirality : 0.039 0.155 2947 Planarity : 0.003 0.053 3270 Dihedral : 3.827 17.167 2531 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.32 % Allowed : 11.62 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2313 helix: 2.34 (0.15), residues: 1283 sheet: -0.20 (0.40), residues: 176 loop : -1.28 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1880 HIS 0.004 0.001 HIS A2059 PHE 0.018 0.001 PHE A1578 TYR 0.021 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 234 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: A 344 ASP cc_start: 0.8321 (m-30) cc_final: 0.8094 (m-30) REVERT: A 523 ASP cc_start: 0.8172 (t0) cc_final: 0.7865 (t0) REVERT: A 689 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7513 (pp) REVERT: A 819 LYS cc_start: 0.7390 (ptpt) cc_final: 0.7041 (pttp) REVERT: A 997 ASP cc_start: 0.8095 (t70) cc_final: 0.7792 (t70) REVERT: A 1514 ASP cc_start: 0.7763 (t70) cc_final: 0.7387 (t0) REVERT: A 1770 LEU cc_start: 0.8402 (mp) cc_final: 0.7649 (tp) REVERT: A 1795 MET cc_start: 0.8005 (ptm) cc_final: 0.7575 (ptm) REVERT: A 2188 TRP cc_start: 0.8191 (m100) cc_final: 0.7505 (m100) REVERT: A 2198 MET cc_start: 0.7744 (mmm) cc_final: 0.7412 (mmm) REVERT: B 577 ASN cc_start: 0.7863 (m110) cc_final: 0.7488 (m110) outliers start: 27 outliers final: 23 residues processed: 226 average time/residue: 0.3264 time to fit residues: 113.0897 Evaluate side-chains 231 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 335 SER 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 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1099 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 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2083 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 585 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.1980 chunk 218 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 151 optimal weight: 0.1980 chunk 229 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 18 optimal weight: 0.0770 chunk 140 optimal weight: 0.0170 chunk 111 optimal weight: 0.9980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** A1875 ASN ** 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: 0.7615 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 19159 Z= 0.145 Angle : 0.464 7.076 25891 Z= 0.241 Chirality : 0.038 0.151 2947 Planarity : 0.003 0.053 3270 Dihedral : 3.613 17.176 2531 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.75 % Allowed : 12.23 % Favored : 87.02 % 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: 1.50 (0.18), residues: 2313 helix: 2.51 (0.15), residues: 1286 sheet: -0.06 (0.40), residues: 176 loop : -1.24 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1880 HIS 0.007 0.000 HIS A2059 PHE 0.020 0.001 PHE A1578 TYR 0.015 0.001 TYR A 607 ARG 0.007 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 239 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 224 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 344 ASP cc_start: 0.8323 (m-30) cc_final: 0.8075 (m-30) REVERT: A 523 ASP cc_start: 0.8169 (t0) cc_final: 0.7645 (t0) REVERT: A 689 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7196 (pp) REVERT: A 819 LYS cc_start: 0.7144 (ptpt) cc_final: 0.6911 (pttp) REVERT: A 997 ASP cc_start: 0.8091 (t70) cc_final: 0.7826 (t70) REVERT: A 1398 GLU cc_start: 0.8533 (pt0) cc_final: 0.8323 (pm20) REVERT: A 1514 ASP cc_start: 0.7719 (t70) cc_final: 0.7348 (t0) REVERT: A 1770 LEU cc_start: 0.8290 (mp) cc_final: 0.7588 (tp) REVERT: A 1795 MET cc_start: 0.7867 (ptm) cc_final: 0.7473 (ptm) REVERT: A 1962 LYS cc_start: 0.6547 (ptpp) cc_final: 0.6316 (pptt) REVERT: A 2033 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 2188 TRP cc_start: 0.8201 (m100) cc_final: 0.7670 (m100) REVERT: A 2198 MET cc_start: 0.7672 (mmm) cc_final: 0.7377 (mmm) REVERT: B 577 ASN cc_start: 0.7866 (m110) cc_final: 0.7539 (m110) outliers start: 15 outliers final: 13 residues processed: 236 average time/residue: 0.3248 time to fit residues: 116.7103 Evaluate side-chains 224 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 440 SER 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 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2083 THR Chi-restraints excluded: chain A residue 2164 LEU 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: 2.9990 chunk 55 optimal weight: 0.7980 chunk 168 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.138774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104352 restraints weight = 50549.331| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.77 r_work: 0.3164 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19159 Z= 0.184 Angle : 0.482 7.319 25891 Z= 0.250 Chirality : 0.039 0.151 2947 Planarity : 0.003 0.053 3270 Dihedral : 3.648 17.016 2531 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.85 % Allowed : 12.42 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2313 helix: 2.50 (0.15), residues: 1284 sheet: -0.08 (0.40), residues: 177 loop : -1.22 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1880 HIS 0.002 0.001 HIS A1611 PHE 0.017 0.001 PHE A1578 TYR 0.024 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: 3900.21 seconds wall clock time: 70 minutes 47.26 seconds (4247.26 seconds total)