Starting phenix.real_space_refine on Sat Mar 16 20:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/03_2024/8dg7_27417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/03_2024/8dg7_27417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/03_2024/8dg7_27417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/03_2024/8dg7_27417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/03_2024/8dg7_27417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/03_2024/8dg7_27417_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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 P 47 5.49 5 Mg 8 5.21 5 S 81 5.16 5 C 9722 2.51 5 N 2738 2.21 5 O 3013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A ASP 907": "OD1" <-> "OD2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1074": "OD1" <-> "OD2" Residue "A ASP 1098": "OD1" <-> "OD2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1588": "OD1" <-> "OD2" Residue "A TYR 1815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1819": "OE1" <-> "OE2" Residue "A ASP 1841": "OD1" <-> "OD2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2197": "OE1" <-> "OE2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15609 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 13175 Classifications: {'peptide': 1635} Link IDs: {'PTRANS': 98, 'TRANS': 1536} Chain breaks: 14 Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 456 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 7} Link IDs: {'rna3p': 20} Chain: "F" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 532 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1417 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 175} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {' MG': 3} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.75, per 1000 atoms: 0.56 Number of scatterers: 15609 At special positions: 0 Unit cell: (155.21, 126.99, 146.91, 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) S 81 16.00 P 47 15.00 Mg 8 11.99 O 3013 8.00 N 2738 7.00 C 9722 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 12 sheets defined 41.7% alpha, 7.5% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 8.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 40 through 58 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 146 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.848A pdb=" N SER A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.390A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 312 removed outlier: 3.860A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 345 removed outlier: 3.501A pdb=" N ARG A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 504 through 518 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.520A pdb=" N GLU A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.876A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 822 through 826' Processing helix chain 'A' and resid 886 through 903 Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.262A pdb=" N ILE A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1061 removed outlier: 3.592A pdb=" N ASN A1057 " --> pdb=" O ASN A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1107 Processing helix chain 'A' and resid 1118 through 1123 Processing helix chain 'A' and resid 1172 through 1179 Processing helix chain 'A' and resid 1221 through 1229 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1249 through 1256 Processing helix chain 'A' and resid 1258 through 1281 Processing helix chain 'A' and resid 1526 through 1548 removed outlier: 3.933A pdb=" N GLN A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A1540 " --> pdb=" O ASN A1536 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1546 " --> pdb=" O TYR A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1580 Processing helix chain 'A' and resid 1608 through 1615 Processing helix chain 'A' and resid 1624 through 1628 Processing helix chain 'A' and resid 1636 through 1649 Processing helix chain 'A' and resid 1723 through 1730 Processing helix chain 'A' and resid 1733 through 1735 No H-bonds generated for 'chain 'A' and resid 1733 through 1735' Processing helix chain 'A' and resid 1742 through 1763 removed outlier: 3.894A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A1750 " --> pdb=" O THR A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1769 through 1780 removed outlier: 4.181A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1791 Processing helix chain 'A' and resid 1820 through 1823 No H-bonds generated for 'chain 'A' and resid 1820 through 1823' Processing helix chain 'A' and resid 1836 through 1843 Processing helix chain 'A' and resid 1848 through 1853 Processing helix chain 'A' and resid 1900 through 1930 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1982 through 1989 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2008 through 2014 Processing helix chain 'A' and resid 2029 through 2048 removed outlier: 3.745A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2064 removed outlier: 3.691A pdb=" N LEU A2062 " --> pdb=" O ALA A2058 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2078 Processing helix chain 'A' and resid 2082 through 2084 No H-bonds generated for 'chain 'A' and resid 2082 through 2084' Processing helix chain 'A' and resid 2090 through 2105 Processing helix chain 'A' and resid 2132 through 2149 removed outlier: 3.673A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2173 removed outlier: 4.160A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2179 through 2185 Processing helix chain 'A' and resid 2224 through 2238 Processing helix chain 'K' and resid 136 through 147 removed outlier: 4.257A pdb=" N ARG K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 204 Processing helix chain 'K' and resid 359 through 372 Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 394 through 404 Processing helix chain 'K' and resid 444 through 463 Processing sheet with id= A, first strand: chain 'A' and resid 220 through 225 removed outlier: 3.770A pdb=" N HIS A 610 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 613 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 527 through 529 removed outlier: 6.439A pdb=" N VAL A 565 " --> pdb=" O GLN A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 849 through 855 Processing sheet with id= D, first strand: chain 'A' and resid 952 through 956 Processing sheet with id= E, first strand: chain 'A' and resid 1095 through 1097 removed outlier: 10.912A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.542A pdb=" N MET A1137 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 4.149A pdb=" N GLN A1235 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1936 through 1941 removed outlier: 3.690A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2209 through 2211 Processing sheet with id= J, first strand: chain 'A' and resid 64 through 66 removed outlier: 7.354A pdb=" N VAL A 66 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A 138 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 152 through 155 removed outlier: 4.184A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE K 180 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 409 through 414 removed outlier: 4.759A pdb=" N GLN K 424 " --> pdb=" O ILE K 414 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4293 1.33 - 1.46: 4242 1.46 - 1.59: 7304 1.59 - 1.71: 85 1.71 - 1.84: 110 Bond restraints: 16034 Sorted by residual: bond pdb=" CG PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.92e+00 bond pdb=" C GLY A 879 " pdb=" N LEU A 880 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.24e+00 bond pdb=" CB PRO A 78 " pdb=" CG PRO A 78 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.06e+00 bond pdb=" C SER A 871 " pdb=" N PRO A 872 " ideal model delta sigma weight residual 1.331 1.351 -0.019 7.90e-03 1.60e+04 5.96e+00 bond pdb=" CA GLU A 926 " pdb=" CB GLU A 926 " ideal model delta sigma weight residual 1.522 1.560 -0.038 1.86e-02 2.89e+03 4.13e+00 ... (remaining 16029 not shown) Histogram of bond angle deviations from ideal: 95.24 - 104.02: 427 104.02 - 112.81: 8552 112.81 - 121.60: 9291 121.60 - 130.39: 3574 130.39 - 139.17: 101 Bond angle restraints: 21945 Sorted by residual: angle pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 112.00 98.76 13.24 1.40e+00 5.10e-01 8.95e+01 angle pdb=" CA LEU A1177 " pdb=" CB LEU A1177 " pdb=" CG LEU A1177 " ideal model delta sigma weight residual 116.30 137.81 -21.51 3.50e+00 8.16e-02 3.78e+01 angle pdb=" CA LEU A1642 " pdb=" CB LEU A1642 " pdb=" CG LEU A1642 " ideal model delta sigma weight residual 116.30 136.89 -20.59 3.50e+00 8.16e-02 3.46e+01 angle pdb=" C LEU A 116 " pdb=" N ARG A 117 " pdb=" CA ARG A 117 " ideal model delta sigma weight residual 122.38 139.17 -16.79 2.90e+00 1.19e-01 3.35e+01 angle pdb=" N PHE A2171 " pdb=" CA PHE A2171 " pdb=" CB PHE A2171 " ideal model delta sigma weight residual 110.28 119.13 -8.85 1.55e+00 4.16e-01 3.26e+01 ... (remaining 21940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8202 17.80 - 35.59: 1140 35.59 - 53.39: 351 53.39 - 71.18: 92 71.18 - 88.98: 27 Dihedral angle restraints: 9812 sinusoidal: 4477 harmonic: 5335 Sorted by residual: dihedral pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta harmonic sigma weight residual 180.00 125.96 54.04 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA THR A1654 " pdb=" C THR A1654 " pdb=" N TYR A1655 " pdb=" CA TYR A1655 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA MET K 462 " pdb=" C MET K 462 " pdb=" N THR K 463 " pdb=" CA THR K 463 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 9809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2334 0.104 - 0.208: 150 0.208 - 0.313: 10 0.313 - 0.417: 2 0.417 - 0.521: 1 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CB ILE A2180 " pdb=" CA ILE A2180 " pdb=" CG1 ILE A2180 " pdb=" CG2 ILE A2180 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CG LEU A2075 " pdb=" CB LEU A2075 " pdb=" CD1 LEU A2075 " pdb=" CD2 LEU A2075 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2494 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 77 " 0.105 5.00e-02 4.00e+02 1.48e-01 3.50e+01 pdb=" N PRO A 78 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 164 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO A 165 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 362 " -0.061 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO A 363 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " -0.050 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 172 2.56 - 3.15: 11676 3.15 - 3.73: 26216 3.73 - 4.32: 34084 4.32 - 4.90: 55066 Nonbonded interactions: 127214 Sorted by model distance: nonbonded pdb=" OE2 GLU A1745 " pdb="MG MG A2301 " model vdw 1.980 2.170 nonbonded pdb=" OE2 GLU A1908 " pdb="MG MG A2302 " model vdw 1.995 2.170 nonbonded pdb=" OP1 C F 39 " pdb="MG MG A2301 " model vdw 2.001 2.170 nonbonded pdb="MG MG A2304 " pdb=" O1P U5P E 101 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A1749 " pdb="MG MG A2302 " model vdw 2.034 2.170 ... (remaining 127209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 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: 17.590 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 48.550 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 0.007 0.123 16034 Z= 0.427 Angle : 1.111 21.512 21945 Z= 0.554 Chirality : 0.056 0.521 2497 Planarity : 0.009 0.148 2661 Dihedral : 18.490 88.981 6344 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.65 % Favored : 91.24 % Rotamer: Outliers : 1.24 % Allowed : 31.43 % Favored : 67.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1780 helix: -1.45 (0.16), residues: 811 sheet: -2.09 (0.36), residues: 190 loop : -2.04 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A1929 HIS 0.011 0.002 HIS A1896 PHE 0.039 0.003 PHE A2171 TYR 0.037 0.003 TYR A 529 ARG 0.006 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7983 (tmm) REVERT: A 1769 GLU cc_start: 0.6320 (pp20) cc_final: 0.5959 (pm20) REVERT: A 1778 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8269 (mmmm) REVERT: K 194 HIS cc_start: 0.6352 (t70) cc_final: 0.5383 (m170) REVERT: K 448 GLN cc_start: 0.7664 (tm130) cc_final: 0.7248 (tm-30) outliers start: 20 outliers final: 10 residues processed: 165 average time/residue: 0.2949 time to fit residues: 74.0012 Evaluate side-chains 152 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1815 TYR Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 2094 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.0010 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16034 Z= 0.175 Angle : 0.609 12.159 21945 Z= 0.298 Chirality : 0.039 0.168 2497 Planarity : 0.005 0.070 2661 Dihedral : 12.868 81.527 2739 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 4.16 % Allowed : 28.57 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.81 (0.19), residues: 1780 helix: -0.32 (0.17), residues: 813 sheet: -1.90 (0.38), residues: 175 loop : -1.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1929 HIS 0.010 0.001 HIS K 450 PHE 0.011 0.001 PHE A1552 TYR 0.012 0.001 TYR A1655 ARG 0.002 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 147 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: A 765 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8900 (tptp) REVERT: A 801 PHE cc_start: 0.4008 (OUTLIER) cc_final: 0.3534 (m-80) REVERT: A 899 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: A 1240 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: K 194 HIS cc_start: 0.6324 (t70) cc_final: 0.5394 (m170) outliers start: 67 outliers final: 29 residues processed: 202 average time/residue: 0.2702 time to fit residues: 83.0976 Evaluate side-chains 164 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 765 LYS Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 174 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.0970 chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16034 Z= 0.178 Angle : 0.596 12.820 21945 Z= 0.288 Chirality : 0.039 0.173 2497 Planarity : 0.004 0.063 2661 Dihedral : 12.578 82.714 2721 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.53 % Favored : 92.30 % Rotamer: Outliers : 5.47 % Allowed : 27.70 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.41 (0.19), residues: 1780 helix: 0.14 (0.18), residues: 815 sheet: -2.03 (0.37), residues: 185 loop : -1.79 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1929 HIS 0.006 0.001 HIS A 901 PHE 0.022 0.001 PHE K 407 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 137 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: A 801 PHE cc_start: 0.3981 (OUTLIER) cc_final: 0.3519 (m-80) REVERT: A 899 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: A 1118 ASP cc_start: 0.7267 (p0) cc_final: 0.5958 (m-30) REVERT: A 1240 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: A 1289 ILE cc_start: 0.4955 (OUTLIER) cc_final: 0.4099 (tp) REVERT: A 1669 ASP cc_start: 0.4750 (OUTLIER) cc_final: 0.3722 (p0) REVERT: A 2036 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7116 (t0) REVERT: A 2171 PHE cc_start: 0.6867 (m-80) cc_final: 0.6556 (m-80) REVERT: K 194 HIS cc_start: 0.6421 (t70) cc_final: 0.5418 (m170) outliers start: 88 outliers final: 49 residues processed: 212 average time/residue: 0.2654 time to fit residues: 85.7315 Evaluate side-chains 180 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 124 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 174 LYS Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 GLN ** A1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16034 Z= 0.397 Angle : 0.732 13.878 21945 Z= 0.361 Chirality : 0.045 0.281 2497 Planarity : 0.005 0.065 2661 Dihedral : 12.735 83.780 2719 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.16 % Favored : 90.67 % Rotamer: Outliers : 7.27 % Allowed : 27.14 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.70 (0.19), residues: 1780 helix: -0.13 (0.18), residues: 811 sheet: -2.15 (0.37), residues: 181 loop : -1.90 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1252 HIS 0.011 0.002 HIS K 450 PHE 0.021 0.002 PHE A2033 TYR 0.017 0.002 TYR A 149 ARG 0.005 0.001 ARG A2078 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 138 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 140 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7392 (pp) REVERT: A 529 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.7049 (p90) REVERT: A 801 PHE cc_start: 0.3985 (OUTLIER) cc_final: 0.3505 (m-80) REVERT: A 1118 ASP cc_start: 0.7288 (p0) cc_final: 0.5895 (m-30) REVERT: A 1289 ILE cc_start: 0.5138 (OUTLIER) cc_final: 0.4257 (tp) REVERT: A 1669 ASP cc_start: 0.5152 (OUTLIER) cc_final: 0.3937 (p0) REVERT: A 1670 HIS cc_start: 0.4513 (OUTLIER) cc_final: 0.4003 (m-70) REVERT: A 2031 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7380 (tt) REVERT: A 2036 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7437 (t0) REVERT: A 2098 ARG cc_start: 0.6214 (ttm-80) cc_final: 0.5851 (ttp80) outliers start: 117 outliers final: 75 residues processed: 238 average time/residue: 0.2531 time to fit residues: 92.9047 Evaluate side-chains 213 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 129 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1532 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16034 Z= 0.209 Angle : 0.629 14.478 21945 Z= 0.305 Chirality : 0.040 0.172 2497 Planarity : 0.004 0.063 2661 Dihedral : 12.535 83.804 2719 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.42 % Favored : 92.42 % Rotamer: Outliers : 7.14 % Allowed : 27.45 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.29 (0.19), residues: 1780 helix: 0.22 (0.18), residues: 814 sheet: -1.87 (0.38), residues: 171 loop : -1.74 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1929 HIS 0.008 0.001 HIS K 450 PHE 0.016 0.001 PHE K 169 TYR 0.013 0.001 TYR A 325 ARG 0.004 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 145 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5381 (mtp180) REVERT: A 53 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 140 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7336 (pp) REVERT: A 200 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5175 (tt) REVERT: A 529 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6882 (p90) REVERT: A 592 THR cc_start: 0.6553 (OUTLIER) cc_final: 0.6212 (p) REVERT: A 801 PHE cc_start: 0.3876 (OUTLIER) cc_final: 0.3433 (m-80) REVERT: A 828 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 1112 MET cc_start: 0.7143 (tpp) cc_final: 0.6927 (tpt) REVERT: A 1118 ASP cc_start: 0.7119 (p0) cc_final: 0.5794 (m-30) REVERT: A 1240 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: A 1289 ILE cc_start: 0.5168 (OUTLIER) cc_final: 0.4293 (tp) REVERT: A 1634 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7897 (tp) REVERT: A 1669 ASP cc_start: 0.4884 (OUTLIER) cc_final: 0.3739 (p0) REVERT: A 1670 HIS cc_start: 0.4356 (OUTLIER) cc_final: 0.3852 (m-70) REVERT: A 1754 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 1953 SER cc_start: 0.6934 (OUTLIER) cc_final: 0.6585 (p) REVERT: A 2036 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7253 (t0) REVERT: K 170 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5830 (mtp180) outliers start: 115 outliers final: 70 residues processed: 241 average time/residue: 0.2674 time to fit residues: 97.6228 Evaluate side-chains 218 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 132 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 458 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0970 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16034 Z= 0.190 Angle : 0.626 13.840 21945 Z= 0.300 Chirality : 0.040 0.182 2497 Planarity : 0.004 0.062 2661 Dihedral : 12.445 84.855 2719 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.36 % Favored : 92.47 % Rotamer: Outliers : 7.45 % Allowed : 27.08 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.09 (0.20), residues: 1780 helix: 0.39 (0.18), residues: 821 sheet: -1.95 (0.38), residues: 179 loop : -1.60 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.022 0.001 PHE A 248 TYR 0.013 0.001 TYR A 325 ARG 0.007 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 140 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5328 (mtp180) REVERT: A 53 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 592 THR cc_start: 0.6534 (OUTLIER) cc_final: 0.6190 (p) REVERT: A 801 PHE cc_start: 0.3862 (OUTLIER) cc_final: 0.3432 (m-80) REVERT: A 828 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7128 (tp) REVERT: A 1118 ASP cc_start: 0.7000 (p0) cc_final: 0.5671 (m-30) REVERT: A 1240 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6091 (mp0) REVERT: A 1289 ILE cc_start: 0.5236 (OUTLIER) cc_final: 0.4372 (tp) REVERT: A 1634 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 1669 ASP cc_start: 0.4768 (OUTLIER) cc_final: 0.3719 (p0) REVERT: A 1670 HIS cc_start: 0.4275 (OUTLIER) cc_final: 0.3754 (m-70) REVERT: A 1953 SER cc_start: 0.6843 (OUTLIER) cc_final: 0.6456 (p) REVERT: A 2036 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7258 (t0) REVERT: A 2102 ILE cc_start: 0.7168 (tp) cc_final: 0.6963 (tp) REVERT: A 2151 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.5818 (mtt) REVERT: K 170 ARG cc_start: 0.5993 (mtp180) cc_final: 0.5734 (mtp180) REVERT: K 394 TYR cc_start: 0.4241 (m-80) cc_final: 0.3808 (m-80) outliers start: 120 outliers final: 79 residues processed: 240 average time/residue: 0.2681 time to fit residues: 97.8851 Evaluate side-chains 227 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 135 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 458 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16034 Z= 0.190 Angle : 0.637 14.813 21945 Z= 0.302 Chirality : 0.040 0.214 2497 Planarity : 0.004 0.061 2661 Dihedral : 12.401 86.037 2719 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.42 % Favored : 92.42 % Rotamer: Outliers : 6.71 % Allowed : 27.33 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.97 (0.20), residues: 1780 helix: 0.52 (0.18), residues: 819 sheet: -1.89 (0.38), residues: 179 loop : -1.56 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.015 0.001 PHE A1149 TYR 0.015 0.001 TYR A 325 ARG 0.006 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 139 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5353 (mtp180) REVERT: A 53 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: A 84 MET cc_start: 0.7547 (tpp) cc_final: 0.7325 (tpp) REVERT: A 592 THR cc_start: 0.6495 (OUTLIER) cc_final: 0.6158 (p) REVERT: A 801 PHE cc_start: 0.3931 (OUTLIER) cc_final: 0.3506 (m-80) REVERT: A 828 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7091 (tp) REVERT: A 899 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: A 1118 ASP cc_start: 0.7014 (p0) cc_final: 0.5689 (m-30) REVERT: A 1211 ARG cc_start: 0.4281 (OUTLIER) cc_final: 0.3719 (mtm110) REVERT: A 1289 ILE cc_start: 0.5251 (OUTLIER) cc_final: 0.4372 (tp) REVERT: A 1634 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 1669 ASP cc_start: 0.4704 (OUTLIER) cc_final: 0.3666 (p0) REVERT: A 1670 HIS cc_start: 0.4224 (OUTLIER) cc_final: 0.3673 (m-70) REVERT: A 1953 SER cc_start: 0.6822 (OUTLIER) cc_final: 0.6442 (p) REVERT: A 2036 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7263 (t0) REVERT: A 2151 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.5965 (mtt) REVERT: A 2169 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: K 170 ARG cc_start: 0.5979 (mtp180) cc_final: 0.5718 (mtp180) REVERT: K 394 TYR cc_start: 0.4264 (m-80) cc_final: 0.3744 (m-80) outliers start: 108 outliers final: 77 residues processed: 228 average time/residue: 0.2537 time to fit residues: 88.4996 Evaluate side-chains 227 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 135 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2169 GLU Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 443 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16034 Z= 0.183 Angle : 0.632 14.376 21945 Z= 0.299 Chirality : 0.040 0.184 2497 Planarity : 0.004 0.061 2661 Dihedral : 12.373 87.341 2719 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.02 % Favored : 92.81 % Rotamer: Outliers : 6.71 % Allowed : 27.64 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.85 (0.20), residues: 1780 helix: 0.65 (0.18), residues: 816 sheet: -1.71 (0.39), residues: 172 loop : -1.57 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.015 0.001 PHE A2171 TYR 0.017 0.001 TYR A 325 ARG 0.005 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 142 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5396 (mtp180) REVERT: A 53 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 84 MET cc_start: 0.7544 (tpp) cc_final: 0.7322 (tpp) REVERT: A 592 THR cc_start: 0.6487 (OUTLIER) cc_final: 0.6196 (p) REVERT: A 801 PHE cc_start: 0.3892 (OUTLIER) cc_final: 0.3491 (m-80) REVERT: A 828 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7105 (tp) REVERT: A 899 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7077 (tp30) REVERT: A 1102 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6777 (tp) REVERT: A 1118 ASP cc_start: 0.7007 (p0) cc_final: 0.5659 (m-30) REVERT: A 1211 ARG cc_start: 0.4208 (OUTLIER) cc_final: 0.3678 (mtm110) REVERT: A 1240 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: A 1289 ILE cc_start: 0.5235 (OUTLIER) cc_final: 0.4363 (tp) REVERT: A 1634 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 1655 TYR cc_start: 0.2057 (OUTLIER) cc_final: 0.1461 (p90) REVERT: A 1669 ASP cc_start: 0.4729 (OUTLIER) cc_final: 0.3745 (p0) REVERT: A 1670 HIS cc_start: 0.4118 (OUTLIER) cc_final: 0.3530 (m-70) REVERT: A 1953 SER cc_start: 0.6867 (OUTLIER) cc_final: 0.6474 (p) REVERT: A 2036 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7233 (t0) REVERT: A 2151 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.6090 (mmt) REVERT: A 2169 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: K 170 ARG cc_start: 0.6020 (mtp180) cc_final: 0.5767 (mtp180) REVERT: K 194 HIS cc_start: 0.6375 (OUTLIER) cc_final: 0.5506 (m170) REVERT: K 394 TYR cc_start: 0.4321 (m-80) cc_final: 0.3801 (m-80) outliers start: 108 outliers final: 76 residues processed: 233 average time/residue: 0.2578 time to fit residues: 93.3823 Evaluate side-chains 228 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 133 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1953 SER Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2169 GLU Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 194 HIS Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 443 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16034 Z= 0.319 Angle : 0.703 15.817 21945 Z= 0.338 Chirality : 0.043 0.328 2497 Planarity : 0.005 0.062 2661 Dihedral : 12.474 88.261 2719 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.71 % Favored : 91.12 % Rotamer: Outliers : 6.77 % Allowed : 27.76 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.13 (0.20), residues: 1780 helix: 0.40 (0.18), residues: 808 sheet: -2.00 (0.38), residues: 185 loop : -1.62 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1929 HIS 0.007 0.001 HIS K 450 PHE 0.024 0.002 PHE A2171 TYR 0.016 0.002 TYR A2028 ARG 0.004 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 132 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5358 (mtp180) REVERT: A 53 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: A 84 MET cc_start: 0.7520 (tpp) cc_final: 0.7274 (tpp) REVERT: A 592 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6189 (p) REVERT: A 801 PHE cc_start: 0.3913 (OUTLIER) cc_final: 0.3486 (m-80) REVERT: A 828 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7138 (tp) REVERT: A 1102 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6824 (tp) REVERT: A 1118 ASP cc_start: 0.7073 (p0) cc_final: 0.5733 (m-30) REVERT: A 1240 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: A 1289 ILE cc_start: 0.5233 (OUTLIER) cc_final: 0.4373 (tp) REVERT: A 1634 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 1669 ASP cc_start: 0.5085 (OUTLIER) cc_final: 0.4047 (p0) REVERT: A 1670 HIS cc_start: 0.4320 (OUTLIER) cc_final: 0.3792 (m-70) REVERT: A 2031 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7301 (tt) REVERT: A 2036 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7372 (t0) REVERT: A 2151 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6309 (mtt) REVERT: K 170 ARG cc_start: 0.6041 (mtp180) cc_final: 0.5816 (mtp180) REVERT: K 394 TYR cc_start: 0.4265 (m-80) cc_final: 0.3675 (m-80) outliers start: 109 outliers final: 83 residues processed: 222 average time/residue: 0.2633 time to fit residues: 89.5689 Evaluate side-chains 228 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 131 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1938 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 194 HIS Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.0070 chunk 107 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 113 optimal weight: 0.0770 chunk 89 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 GLN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16034 Z= 0.157 Angle : 0.638 15.193 21945 Z= 0.301 Chirality : 0.040 0.262 2497 Planarity : 0.004 0.060 2661 Dihedral : 12.353 88.593 2719 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.57 % Favored : 93.26 % Rotamer: Outliers : 5.03 % Allowed : 29.38 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.75 (0.20), residues: 1780 helix: 0.74 (0.18), residues: 811 sheet: -1.74 (0.38), residues: 181 loop : -1.50 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.014 0.001 PHE A 248 TYR 0.017 0.001 TYR A1815 ARG 0.006 0.000 ARG A2098 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 147 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.5527 (mtp180) REVERT: A 53 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 801 PHE cc_start: 0.3805 (OUTLIER) cc_final: 0.3412 (m-80) REVERT: A 1102 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6791 (tp) REVERT: A 1118 ASP cc_start: 0.6908 (p0) cc_final: 0.5604 (m-30) REVERT: A 1240 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: A 1669 ASP cc_start: 0.4472 (OUTLIER) cc_final: 0.3472 (p0) REVERT: A 1670 HIS cc_start: 0.4076 (OUTLIER) cc_final: 0.3502 (m-70) REVERT: A 2036 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7100 (t0) REVERT: A 2169 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: K 170 ARG cc_start: 0.5955 (mtp180) cc_final: 0.5708 (mtp180) REVERT: K 194 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5587 (m170) REVERT: K 394 TYR cc_start: 0.4183 (m-80) cc_final: 0.3621 (m-80) REVERT: K 448 GLN cc_start: 0.7854 (tm130) cc_final: 0.7225 (tp40) outliers start: 81 outliers final: 60 residues processed: 213 average time/residue: 0.2647 time to fit residues: 86.2706 Evaluate side-chains 210 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 140 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1670 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2169 GLU Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 194 HIS Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 443 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.165026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.133213 restraints weight = 30693.071| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.06 r_work: 0.3844 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16034 Z= 0.174 Angle : 0.638 15.646 21945 Z= 0.299 Chirality : 0.040 0.272 2497 Planarity : 0.004 0.060 2661 Dihedral : 12.266 89.945 2717 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.91 % Favored : 92.92 % Rotamer: Outliers : 4.53 % Allowed : 30.06 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.64 (0.20), residues: 1780 helix: 0.84 (0.18), residues: 811 sheet: -1.65 (0.39), residues: 181 loop : -1.45 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.013 0.001 PHE A2171 TYR 0.016 0.001 TYR A1815 ARG 0.005 0.000 ARG A2098 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3559.59 seconds wall clock time: 65 minutes 15.74 seconds (3915.74 seconds total)