Starting phenix.real_space_refine on Wed Mar 4 20:00:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dga_27420/03_2026/8dga_27420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dga_27420/03_2026/8dga_27420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dga_27420/03_2026/8dga_27420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dga_27420/03_2026/8dga_27420.map" model { file = "/net/cci-nas-00/data/ceres_data/8dga_27420/03_2026/8dga_27420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dga_27420/03_2026/8dga_27420.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.028 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: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 80 5.16 5 C 9663 2.51 5 N 2710 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15473 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1629, 13162 Classifications: {'peptide': 1629} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 1532} Chain breaks: 11 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 414 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 16} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1424 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 3.52, per 1000 atoms: 0.23 Number of scatterers: 15473 At special positions: 0 Unit cell: (158.53, 129.48, 145.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 42 15.00 O 2978 8.00 N 2710 7.00 C 9663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 576.4 milliseconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3460 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 48.6% alpha, 10.2% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 39 through 61 removed outlier: 4.137A pdb=" N ARG A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.612A pdb=" N TYR A 111 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 159 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 232 through 252 removed outlier: 4.141A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.088A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 4.199A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 344 removed outlier: 4.128A pdb=" N PHE A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.733A pdb=" N TYR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 374 Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 763 through 785 removed outlier: 3.538A pdb=" N CYS A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 4.030A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 835 removed outlier: 3.522A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 903 removed outlier: 3.725A pdb=" N ALA A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.750A pdb=" N GLU A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 940 Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 1000 through 1004 Processing helix chain 'A' and resid 1045 through 1062 Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1124 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.689A pdb=" N PHE A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 3.749A pdb=" N TYR A1180 " --> pdb=" O TYR A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1230 removed outlier: 4.083A pdb=" N LYS A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1229 " --> pdb=" O ARG A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1538 through 1550 Processing helix chain 'A' and resid 1565 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1622 through 1629 Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1741 through 1764 Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.746A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1793 removed outlier: 3.514A pdb=" N LEU A1785 " --> pdb=" O ALA A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1798 removed outlier: 3.860A pdb=" N MET A1798 " --> pdb=" O GLY A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1825 removed outlier: 3.511A pdb=" N ALA A1823 " --> pdb=" O GLU A1819 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1825 " --> pdb=" O GLU A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1856 Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 Processing helix chain 'A' and resid 1993 through 2001 Processing helix chain 'A' and resid 2006 through 2014 removed outlier: 4.104A pdb=" N LEU A2010 " --> pdb=" O ASP A2006 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.955A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 removed outlier: 3.574A pdb=" N HIS A2079 " --> pdb=" O LEU A2075 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2105 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.754A pdb=" N GLY A2135 " --> pdb=" O PRO A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2174 removed outlier: 4.161A pdb=" N VAL A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix removed outlier: 4.439A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2187 removed outlier: 3.807A pdb=" N LEU A2183 " --> pdb=" O PRO A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2223 through 2239 removed outlier: 3.728A pdb=" N ALA A2227 " --> pdb=" O ASN A2223 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 188 through 205 removed outlier: 3.890A pdb=" N LEU K 204 " --> pdb=" O LEU K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 374 removed outlier: 3.740A pdb=" N PHE K 367 " --> pdb=" O LYS K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 393 through 405 Processing helix chain 'K' and resid 443 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.471A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 140 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 68 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU A 136 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU A 172 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 138 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU A 174 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 140 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 34 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 224 removed outlier: 5.732A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR A 222 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 496 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 497 " --> pdb=" O GLY A 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 877 through 878 removed outlier: 4.339A pdb=" N CYS A 850 " --> pdb=" O MET A1658 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 852 " --> pdb=" O ASN A1656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 952 through 956 Processing sheet with id=AA5, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 6.859A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 6.859A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A1087 " --> pdb=" O GLY A1007 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1153 through 1155 Processing sheet with id=AA8, first strand: chain 'A' and resid 1937 through 1941 removed outlier: 3.836A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2192 through 2193 removed outlier: 3.618A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2205 through 2206 Processing sheet with id=AB2, first strand: chain 'K' and resid 152 through 158 removed outlier: 3.805A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 409 through 412 685 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 1.75 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: 3969 1.33 - 1.46: 3438 1.46 - 1.58: 8294 1.58 - 1.70: 83 1.70 - 1.82: 109 Bond restraints: 15893 Sorted by residual: bond pdb=" O5' U5P E 101 " pdb=" P U5P E 101 " ideal model delta sigma weight residual 1.711 1.590 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C GLU A 931 " pdb=" N PRO A 932 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.38e-02 5.25e+03 6.95e+00 bond pdb=" CG LEU A1915 " pdb=" CD1 LEU A1915 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.70e+00 bond pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " ideal model delta sigma weight residual 1.520 1.591 -0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" CG LEU A2147 " pdb=" CD1 LEU A2147 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.52e+00 ... (remaining 15888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 21231 3.37 - 6.75: 418 6.75 - 10.12: 58 10.12 - 13.50: 14 13.50 - 16.87: 1 Bond angle restraints: 21722 Sorted by residual: angle pdb=" C ARG A 866 " pdb=" N LEU A 867 " pdb=" CA LEU A 867 " ideal model delta sigma weight residual 121.03 129.62 -8.59 1.60e+00 3.91e-01 2.88e+01 angle pdb=" C CYS A 107 " pdb=" N TRP A 108 " pdb=" CA TRP A 108 " ideal model delta sigma weight residual 120.72 129.39 -8.67 1.67e+00 3.59e-01 2.69e+01 angle pdb=" N GLU A 196 " pdb=" CA GLU A 196 " pdb=" CB GLU A 196 " ideal model delta sigma weight residual 110.16 117.75 -7.59 1.48e+00 4.57e-01 2.63e+01 angle pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " pdb=" CD GLN A2053 " ideal model delta sigma weight residual 112.60 121.05 -8.45 1.70e+00 3.46e-01 2.47e+01 angle pdb=" N ASP A2123 " pdb=" CA ASP A2123 " pdb=" C ASP A2123 " ideal model delta sigma weight residual 112.92 106.96 5.96 1.23e+00 6.61e-01 2.35e+01 ... (remaining 21717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8735 17.90 - 35.80: 782 35.80 - 53.70: 149 53.70 - 71.59: 61 71.59 - 89.49: 17 Dihedral angle restraints: 9744 sinusoidal: 4419 harmonic: 5325 Sorted by residual: dihedral pdb=" CA VAL A 14 " pdb=" C VAL A 14 " pdb=" N PHE A 15 " pdb=" CA PHE A 15 " ideal model delta harmonic sigma weight residual -180.00 -119.71 -60.29 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LEU A2117 " pdb=" C LEU A2117 " pdb=" N SER A2118 " pdb=" CA SER A2118 " ideal model delta harmonic sigma weight residual 180.00 132.42 47.58 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA ILE A1829 " pdb=" C ILE A1829 " pdb=" N PRO A1830 " pdb=" CA PRO A1830 " ideal model delta harmonic sigma weight residual 180.00 145.26 34.74 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2253 0.105 - 0.211: 186 0.211 - 0.316: 15 0.316 - 0.421: 3 0.421 - 0.527: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CG LEU A 496 " pdb=" CB LEU A 496 " pdb=" CD1 LEU A 496 " pdb=" CD2 LEU A 496 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CB ILE A1829 " pdb=" CA ILE A1829 " pdb=" CG1 ILE A1829 " pdb=" CG2 ILE A1829 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE A1010 " pdb=" CA ILE A1010 " pdb=" CG1 ILE A1010 " pdb=" CG2 ILE A1010 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2456 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 108 " 0.058 2.00e-02 2.50e+03 6.16e-02 9.49e+01 pdb=" CG TRP A 108 " -0.154 2.00e-02 2.50e+03 pdb=" CD1 TRP A 108 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TRP A 108 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 108 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 108 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 108 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 108 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 108 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 848 " -0.032 2.00e-02 2.50e+03 4.46e-02 4.97e+01 pdb=" CG TRP A 848 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 848 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP A 848 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 848 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 848 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 848 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 848 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 848 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 848 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A2053 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN A2053 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN A2053 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A2054 " 0.021 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1725 2.75 - 3.29: 15109 3.29 - 3.82: 27254 3.82 - 4.36: 31780 4.36 - 4.90: 51164 Nonbonded interactions: 127032 Sorted by model distance: nonbonded pdb=" O ARG A1207 " pdb=" O2' A F 50 " model vdw 2.210 3.040 nonbonded pdb=" O LEU K 459 " pdb=" OG1 THR K 463 " model vdw 2.264 3.040 nonbonded pdb=" O PHE A 841 " pdb=" OG SER A2089 " model vdw 2.266 3.040 nonbonded pdb=" O VAL A1767 " pdb=" NH1 ARG A2030 " model vdw 2.283 3.120 nonbonded pdb=" O GLY A 294 " pdb=" OG1 THR A 298 " model vdw 2.283 3.040 ... (remaining 127027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 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 0.121 15894 Z= 0.316 Angle : 1.166 16.872 21722 Z= 0.598 Chirality : 0.062 0.527 2459 Planarity : 0.009 0.121 2656 Dihedral : 15.030 89.493 6284 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.01 % Favored : 92.65 % Rotamer: Outliers : 0.12 % Allowed : 0.81 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.18), residues: 1783 helix: -1.42 (0.15), residues: 818 sheet: -0.79 (0.39), residues: 160 loop : -1.77 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A2045 TYR 0.031 0.004 TYR A1175 PHE 0.047 0.004 PHE A 15 TRP 0.154 0.009 TRP A 108 HIS 0.014 0.002 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00721 (15893) covalent geometry : angle 1.16602 (21722) hydrogen bonds : bond 0.14567 ( 716) hydrogen bonds : angle 6.89311 ( 2059) Misc. bond : bond 0.04738 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1112 MET cc_start: 0.6330 (tpt) cc_final: 0.6048 (tpt) REVERT: A 2151 MET cc_start: 0.7153 (mpp) cc_final: 0.6568 (mpp) REVERT: A 2163 MET cc_start: 0.7367 (mpp) cc_final: 0.6996 (mmt) REVERT: K 405 ASN cc_start: 0.5972 (t160) cc_final: 0.5726 (t0) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.1326 time to fit residues: 36.3125 Evaluate side-chains 119 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS A 885 GLN A1189 GLN A1620 ASN A2016 HIS K 163 HIS K 405 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.170213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.144421 restraints weight = 42706.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.143282 restraints weight = 38825.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.144942 restraints weight = 31049.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.145718 restraints weight = 20871.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.145989 restraints weight = 20764.607| |-----------------------------------------------------------------------------| r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15894 Z= 0.141 Angle : 0.667 14.552 21722 Z= 0.339 Chirality : 0.042 0.246 2459 Planarity : 0.005 0.061 2656 Dihedral : 12.595 96.884 2633 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 1.18 % Allowed : 7.65 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1783 helix: -0.08 (0.17), residues: 830 sheet: -0.70 (0.40), residues: 167 loop : -1.49 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 775 TYR 0.024 0.002 TYR K 458 PHE 0.025 0.002 PHE A 121 TRP 0.047 0.003 TRP A 108 HIS 0.006 0.001 HIS A1833 Details of bonding type rmsd covalent geometry : bond 0.00302 (15893) covalent geometry : angle 0.66694 (21722) hydrogen bonds : bond 0.04473 ( 716) hydrogen bonds : angle 4.95059 ( 2059) Misc. bond : bond 0.00097 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.4094 (mpp) cc_final: 0.3529 (mmt) REVERT: A 560 MET cc_start: 0.4673 (mmp) cc_final: 0.4377 (mmp) REVERT: A 2151 MET cc_start: 0.7032 (mpp) cc_final: 0.6765 (mpp) REVERT: A 2163 MET cc_start: 0.6912 (mpp) cc_final: 0.6621 (mmt) outliers start: 19 outliers final: 13 residues processed: 173 average time/residue: 0.1164 time to fit residues: 31.4421 Evaluate side-chains 139 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 7.9990 chunk 41 optimal weight: 0.0570 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 141 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 101 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS A 770 GLN A 787 ASN A1784 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.168335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.142004 restraints weight = 43147.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.140705 restraints weight = 38528.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142356 restraints weight = 30995.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.143149 restraints weight = 21037.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.143397 restraints weight = 20651.581| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15894 Z= 0.142 Angle : 0.634 12.365 21722 Z= 0.323 Chirality : 0.042 0.209 2459 Planarity : 0.005 0.058 2656 Dihedral : 12.211 96.769 2633 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.83 % Favored : 93.83 % Rotamer: Outliers : 1.87 % Allowed : 10.57 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1783 helix: 0.35 (0.17), residues: 834 sheet: -0.74 (0.40), residues: 172 loop : -1.41 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2181 TYR 0.016 0.002 TYR A1148 PHE 0.020 0.001 PHE K 367 TRP 0.024 0.002 TRP A 108 HIS 0.009 0.001 HIS K 194 Details of bonding type rmsd covalent geometry : bond 0.00315 (15893) covalent geometry : angle 0.63409 (21722) hydrogen bonds : bond 0.04238 ( 716) hydrogen bonds : angle 4.73075 ( 2059) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6070 (mpp) cc_final: 0.5352 (tpp) REVERT: A 108 TRP cc_start: 0.4694 (m-10) cc_final: 0.4459 (m-10) REVERT: A 560 MET cc_start: 0.4796 (mmp) cc_final: 0.4489 (mmp) REVERT: A 2151 MET cc_start: 0.6983 (mpp) cc_final: 0.6653 (mpp) REVERT: A 2163 MET cc_start: 0.7057 (mpp) cc_final: 0.6699 (mmt) REVERT: K 368 HIS cc_start: 0.1579 (m-70) cc_final: 0.1287 (m-70) outliers start: 30 outliers final: 19 residues processed: 163 average time/residue: 0.1220 time to fit residues: 31.2041 Evaluate side-chains 149 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 423 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 25 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 44 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 787 ASN A1620 ASN A1668 ASN A1833 HIS K 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.166224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.140351 restraints weight = 43068.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.139348 restraints weight = 43302.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.141036 restraints weight = 34137.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.141417 restraints weight = 22590.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.141760 restraints weight = 22678.620| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15894 Z= 0.171 Angle : 0.659 10.795 21722 Z= 0.335 Chirality : 0.042 0.201 2459 Planarity : 0.005 0.085 2656 Dihedral : 12.015 95.793 2633 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.45 % Favored : 93.21 % Rotamer: Outliers : 2.30 % Allowed : 12.69 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1783 helix: 0.46 (0.17), residues: 836 sheet: -0.65 (0.40), residues: 172 loop : -1.42 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2098 TYR 0.014 0.002 TYR A 322 PHE 0.019 0.002 PHE K 367 TRP 0.025 0.002 TRP A 848 HIS 0.024 0.001 HIS K 194 Details of bonding type rmsd covalent geometry : bond 0.00388 (15893) covalent geometry : angle 0.65875 (21722) hydrogen bonds : bond 0.04306 ( 716) hydrogen bonds : angle 4.74474 ( 2059) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6143 (mpp) cc_final: 0.5268 (tpp) REVERT: A 560 MET cc_start: 0.4928 (mmp) cc_final: 0.4618 (mmp) REVERT: A 1202 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6868 (t0) REVERT: A 1664 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4293 (m-10) REVERT: A 2151 MET cc_start: 0.7045 (mpp) cc_final: 0.6744 (mpp) REVERT: K 368 HIS cc_start: 0.1739 (m-70) cc_final: 0.1408 (m-70) outliers start: 37 outliers final: 25 residues processed: 165 average time/residue: 0.1175 time to fit residues: 30.1766 Evaluate side-chains 153 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 787 ASN A1896 HIS A2223 ASN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.168317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.143099 restraints weight = 43024.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.142293 restraints weight = 38653.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.143519 restraints weight = 33068.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144363 restraints weight = 22377.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.144492 restraints weight = 21487.022| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15894 Z= 0.121 Angle : 0.602 7.771 21722 Z= 0.308 Chirality : 0.041 0.204 2459 Planarity : 0.005 0.095 2656 Dihedral : 11.771 93.103 2633 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.72 % Favored : 93.94 % Rotamer: Outliers : 1.87 % Allowed : 14.86 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1783 helix: 0.78 (0.18), residues: 834 sheet: -0.54 (0.40), residues: 172 loop : -1.29 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2098 TYR 0.021 0.001 TYR A1148 PHE 0.018 0.001 PHE K 367 TRP 0.019 0.002 TRP A 848 HIS 0.007 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00266 (15893) covalent geometry : angle 0.60178 (21722) hydrogen bonds : bond 0.03851 ( 716) hydrogen bonds : angle 4.52950 ( 2059) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7028 (m) cc_final: 0.6812 (m) REVERT: A 108 TRP cc_start: 0.4583 (m-90) cc_final: 0.4183 (m-10) REVERT: A 560 MET cc_start: 0.4955 (mmp) cc_final: 0.4579 (mmp) REVERT: A 1664 PHE cc_start: 0.4768 (OUTLIER) cc_final: 0.4067 (m-10) REVERT: A 2151 MET cc_start: 0.6901 (mpp) cc_final: 0.6642 (mpp) REVERT: K 164 GLU cc_start: 0.3490 (OUTLIER) cc_final: 0.3136 (pp20) REVERT: K 368 HIS cc_start: 0.1811 (m-70) cc_final: 0.1553 (m-70) outliers start: 30 outliers final: 23 residues processed: 161 average time/residue: 0.1152 time to fit residues: 28.8684 Evaluate side-chains 155 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 56 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 122 optimal weight: 0.0270 chunk 168 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.168664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.142746 restraints weight = 42969.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.142634 restraints weight = 35582.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.143811 restraints weight = 31864.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.143844 restraints weight = 21771.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.144114 restraints weight = 20199.407| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15894 Z= 0.118 Angle : 0.601 15.430 21722 Z= 0.303 Chirality : 0.041 0.202 2459 Planarity : 0.004 0.059 2656 Dihedral : 11.631 91.856 2633 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.17 % Rotamer: Outliers : 2.05 % Allowed : 16.42 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1783 helix: 0.93 (0.18), residues: 836 sheet: -0.63 (0.39), residues: 178 loop : -1.25 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.025 0.001 TYR A1148 PHE 0.018 0.001 PHE K 367 TRP 0.021 0.002 TRP A 848 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00261 (15893) covalent geometry : angle 0.60128 (21722) hydrogen bonds : bond 0.03703 ( 716) hydrogen bonds : angle 4.45063 ( 2059) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7015 (m) cc_final: 0.6768 (m) REVERT: A 84 MET cc_start: 0.6006 (mpp) cc_final: 0.5750 (mpp) REVERT: A 108 TRP cc_start: 0.4864 (m-90) cc_final: 0.4475 (m-10) REVERT: A 560 MET cc_start: 0.4975 (mmp) cc_final: 0.4595 (mmp) REVERT: A 900 LEU cc_start: 0.6543 (mt) cc_final: 0.6270 (mt) REVERT: A 1037 LEU cc_start: 0.5338 (mt) cc_final: 0.5020 (pp) REVERT: A 1593 LEU cc_start: 0.0598 (OUTLIER) cc_final: -0.0241 (mt) REVERT: A 1664 PHE cc_start: 0.4825 (OUTLIER) cc_final: 0.4095 (m-10) REVERT: A 2151 MET cc_start: 0.6859 (mpp) cc_final: 0.6552 (mpp) REVERT: K 164 GLU cc_start: 0.3395 (OUTLIER) cc_final: 0.3009 (pp20) outliers start: 33 outliers final: 22 residues processed: 162 average time/residue: 0.1158 time to fit residues: 29.3298 Evaluate side-chains 155 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 78 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN A1668 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.169007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.143211 restraints weight = 42876.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.142843 restraints weight = 35859.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144237 restraints weight = 29489.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.144430 restraints weight = 20673.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.144664 restraints weight = 20389.730| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15894 Z= 0.114 Angle : 0.604 12.920 21722 Z= 0.304 Chirality : 0.040 0.204 2459 Planarity : 0.004 0.058 2656 Dihedral : 11.571 92.171 2633 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 2.30 % Allowed : 16.73 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1783 helix: 1.11 (0.18), residues: 835 sheet: -0.72 (0.39), residues: 183 loop : -1.18 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2222 TYR 0.032 0.001 TYR A1148 PHE 0.021 0.001 PHE A1554 TRP 0.034 0.002 TRP A1834 HIS 0.014 0.001 HIS K 368 Details of bonding type rmsd covalent geometry : bond 0.00252 (15893) covalent geometry : angle 0.60425 (21722) hydrogen bonds : bond 0.03659 ( 716) hydrogen bonds : angle 4.34557 ( 2059) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6987 (m) cc_final: 0.6730 (m) REVERT: A 84 MET cc_start: 0.5980 (mpp) cc_final: 0.5727 (mpp) REVERT: A 338 LEU cc_start: 0.7484 (tp) cc_final: 0.7118 (pp) REVERT: A 560 MET cc_start: 0.5036 (mmp) cc_final: 0.4691 (mmp) REVERT: A 863 TYR cc_start: 0.4298 (OUTLIER) cc_final: 0.3864 (t80) REVERT: A 900 LEU cc_start: 0.6496 (mt) cc_final: 0.6209 (mt) REVERT: A 1593 LEU cc_start: 0.0830 (OUTLIER) cc_final: -0.0118 (mt) REVERT: A 1664 PHE cc_start: 0.4809 (OUTLIER) cc_final: 0.4081 (m-10) REVERT: A 2151 MET cc_start: 0.6811 (mpp) cc_final: 0.6549 (mpp) REVERT: K 164 GLU cc_start: 0.3312 (OUTLIER) cc_final: 0.2933 (pp20) outliers start: 37 outliers final: 28 residues processed: 162 average time/residue: 0.1105 time to fit residues: 28.1320 Evaluate side-chains 164 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 105 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.168874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.143406 restraints weight = 43249.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.143238 restraints weight = 37482.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.144607 restraints weight = 30319.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.144746 restraints weight = 20786.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.145062 restraints weight = 21069.684| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15894 Z= 0.116 Angle : 0.598 11.979 21722 Z= 0.303 Chirality : 0.040 0.205 2459 Planarity : 0.004 0.056 2656 Dihedral : 11.528 92.258 2633 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.66 % Favored : 94.05 % Rotamer: Outliers : 2.24 % Allowed : 17.23 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1783 helix: 1.23 (0.18), residues: 835 sheet: -0.67 (0.39), residues: 183 loop : -1.18 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.033 0.001 TYR A1148 PHE 0.027 0.001 PHE A1554 TRP 0.033 0.002 TRP A1834 HIS 0.013 0.001 HIS K 368 Details of bonding type rmsd covalent geometry : bond 0.00256 (15893) covalent geometry : angle 0.59811 (21722) hydrogen bonds : bond 0.03616 ( 716) hydrogen bonds : angle 4.31932 ( 2059) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6948 (m) cc_final: 0.6706 (m) REVERT: A 338 LEU cc_start: 0.7317 (tp) cc_final: 0.7099 (pp) REVERT: A 560 MET cc_start: 0.5041 (mmp) cc_final: 0.4683 (mmp) REVERT: A 863 TYR cc_start: 0.4309 (OUTLIER) cc_final: 0.3929 (t80) REVERT: A 900 LEU cc_start: 0.6460 (mt) cc_final: 0.6172 (mt) REVERT: A 1593 LEU cc_start: 0.0575 (OUTLIER) cc_final: -0.0259 (mt) REVERT: A 1664 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.3984 (m-10) REVERT: A 2014 MET cc_start: 0.6693 (mmm) cc_final: 0.6394 (mmm) REVERT: A 2151 MET cc_start: 0.6859 (mpp) cc_final: 0.6590 (mpp) REVERT: K 164 GLU cc_start: 0.3273 (OUTLIER) cc_final: 0.2897 (pp20) outliers start: 36 outliers final: 27 residues processed: 158 average time/residue: 0.1101 time to fit residues: 27.5324 Evaluate side-chains 158 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 6 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 181 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.1980 chunk 31 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1147 GLN A1202 ASN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.165129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.139846 restraints weight = 43071.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.139194 restraints weight = 48427.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.140566 restraints weight = 39258.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.141572 restraints weight = 25955.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.141804 restraints weight = 24717.589| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15894 Z= 0.183 Angle : 0.686 13.928 21722 Z= 0.347 Chirality : 0.043 0.212 2459 Planarity : 0.005 0.057 2656 Dihedral : 11.733 87.601 2633 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.67 % Favored : 93.05 % Rotamer: Outliers : 2.30 % Allowed : 17.66 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1783 helix: 0.95 (0.18), residues: 836 sheet: -0.73 (0.39), residues: 177 loop : -1.33 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 170 TYR 0.028 0.002 TYR A1148 PHE 0.037 0.002 PHE A1554 TRP 0.031 0.002 TRP A1834 HIS 0.018 0.001 HIS K 368 Details of bonding type rmsd covalent geometry : bond 0.00417 (15893) covalent geometry : angle 0.68649 (21722) hydrogen bonds : bond 0.04207 ( 716) hydrogen bonds : angle 4.62059 ( 2059) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5887 (mpp) cc_final: 0.5451 (tpp) REVERT: A 560 MET cc_start: 0.5304 (mmp) cc_final: 0.4920 (mmp) REVERT: A 1593 LEU cc_start: 0.0465 (OUTLIER) cc_final: -0.0511 (mt) REVERT: A 1664 PHE cc_start: 0.4943 (OUTLIER) cc_final: 0.4219 (m-10) REVERT: A 2151 MET cc_start: 0.7119 (mpp) cc_final: 0.6670 (mpp) REVERT: K 164 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.2927 (pp20) REVERT: K 405 ASN cc_start: 0.4187 (t0) cc_final: 0.2863 (m-40) outliers start: 37 outliers final: 27 residues processed: 157 average time/residue: 0.1072 time to fit residues: 26.7921 Evaluate side-chains 152 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 33 optimal weight: 0.0020 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1080 ASN A1543 GLN A1981 ASN A2053 GLN K 366 GLN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.167593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.141558 restraints weight = 42942.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.140572 restraints weight = 37438.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.141911 restraints weight = 31956.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142146 restraints weight = 23169.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.142466 restraints weight = 21865.606| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15894 Z= 0.126 Angle : 0.633 12.695 21722 Z= 0.319 Chirality : 0.041 0.215 2459 Planarity : 0.004 0.056 2656 Dihedral : 11.653 92.394 2633 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.00 % Favored : 93.72 % Rotamer: Outliers : 2.05 % Allowed : 18.41 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1783 helix: 1.13 (0.18), residues: 836 sheet: -0.65 (0.40), residues: 176 loop : -1.24 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 170 TYR 0.034 0.001 TYR A1148 PHE 0.031 0.001 PHE K 367 TRP 0.031 0.002 TRP A1834 HIS 0.016 0.001 HIS K 368 Details of bonding type rmsd covalent geometry : bond 0.00283 (15893) covalent geometry : angle 0.63283 (21722) hydrogen bonds : bond 0.03729 ( 716) hydrogen bonds : angle 4.43182 ( 2059) Misc. bond : bond 0.00009 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.3194 (mmp-170) cc_final: 0.2471 (mmp80) REVERT: A 338 LEU cc_start: 0.7273 (tp) cc_final: 0.6898 (pp) REVERT: A 1593 LEU cc_start: 0.0470 (OUTLIER) cc_final: -0.0457 (mt) REVERT: A 1664 PHE cc_start: 0.4667 (OUTLIER) cc_final: 0.3928 (m-10) REVERT: A 1929 TRP cc_start: 0.7498 (t60) cc_final: 0.6899 (t60) REVERT: A 2151 MET cc_start: 0.6891 (mpp) cc_final: 0.6564 (mpp) REVERT: K 164 GLU cc_start: 0.3193 (OUTLIER) cc_final: 0.2801 (pp20) REVERT: K 405 ASN cc_start: 0.4010 (t0) cc_final: 0.2583 (m-40) outliers start: 33 outliers final: 28 residues processed: 146 average time/residue: 0.1148 time to fit residues: 27.4201 Evaluate side-chains 150 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2053 GLN Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 86 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.167375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.141227 restraints weight = 42931.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.140353 restraints weight = 37511.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.141776 restraints weight = 30879.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.142038 restraints weight = 21514.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.142326 restraints weight = 21268.440| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.344 15894 Z= 0.281 Angle : 0.974 59.200 21722 Z= 0.569 Chirality : 0.046 0.909 2459 Planarity : 0.005 0.106 2656 Dihedral : 11.656 92.392 2633 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.89 % Favored : 93.83 % Rotamer: Outliers : 2.18 % Allowed : 18.41 % Favored : 79.42 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1783 helix: 1.13 (0.18), residues: 836 sheet: -0.65 (0.40), residues: 176 loop : -1.23 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 170 TYR 0.045 0.002 TYR K 458 PHE 0.030 0.001 PHE K 367 TRP 0.029 0.002 TRP A1834 HIS 0.016 0.001 HIS K 368 Details of bonding type rmsd covalent geometry : bond 0.00593 (15893) covalent geometry : angle 0.97375 (21722) hydrogen bonds : bond 0.03733 ( 716) hydrogen bonds : angle 4.43588 ( 2059) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.28 seconds wall clock time: 46 minutes 24.65 seconds (2784.65 seconds total)