Starting phenix.real_space_refine on Sat Sep 12 13:14:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dga_27420/09_2026/8dga_27420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dga_27420/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dga_27420/09_2026/8dga_27420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dga_27420/09_2026/8dga_27420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dga_27420/09_2026/8dga_27420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dga_27420/09_2026/8dga_27420.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dga_27420/09_2026/8dga_27420.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dga_27420/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 3.02, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 483.8 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: 1.77 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: 3.64 Time building geometry restraints manager: 1.77 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=" 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 bond pdb=" C LEU A 867 " pdb=" N PRO A 868 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.25e-02 6.40e+03 5.20e+00 ... (remaining 15888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 21224 3.37 - 6.75: 425 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: 8637 17.90 - 35.80: 774 35.80 - 53.70: 143 53.70 - 71.59: 24 71.59 - 89.49: 8 Dihedral angle restraints: 9586 sinusoidal: 4261 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=" O5' G E 15 " pdb=" C5' G E 15 " pdb=" C4' G E 15 " pdb=" C3' G E 15 " ideal model delta sinusoidal sigma weight residual 180.00 127.17 52.83 3 6.40e+00 2.44e-02 5.03e+01 ... (remaining 9583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2213 0.105 - 0.211: 197 0.211 - 0.316: 44 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: 7.360 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.570 Find NCS groups from input model: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 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 0.093 15894 Z= 0.312 Angle : 1.177 16.872 21722 Z= 0.597 Chirality : 0.069 0.527 2459 Planarity : 0.009 0.121 2656 Dihedral : 13.983 89.493 6126 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/Z covalent geometry : bond 0.00715 / 0.31 (15893) covalent geometry : angle 1.17713 / 0.60 (21722) hydrogen bonds : bond 0.14567 / 9.84 ( 716) hydrogen bonds : angle 6.89311 / 4.86 ( 2059) Misc. bond : bond 0.04738 / 2.49 ( 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 : 0.598 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: 0.1224 time to fit residues: 33.6307 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 : 0.546 ------------------------------------------------------------------------------- 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... A 61 HIS A 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.170299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.144184 restraints weight = 42715.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.143681 restraints weight = 37248.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.144945 restraints weight = 31898.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.144878 restraints weight = 23448.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.145326 restraints weight = 20594.090| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.1604 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= 0.139 Angle : 0.699 14.482 21722 Z= 0.342 Chirality : 0.047 0.376 2459 Planarity : 0.005 0.061 2656 Dihedral : 9.036 68.443 2475 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 1.18 % Allowed : 7.77 % Favored : 91.04 % 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: -1.14 (0.19), residues: 1783 helix: -0.05 (0.17), residues: 830 sheet: -0.69 (0.40), residues: 167 loop : -1.49 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 775 TYR 0.024 0.001 TYR K 458 PHE 0.024 0.002 PHE A1552 TRP 0.044 0.003 TRP A 108 HIS 0.006 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (15893) covalent geometry : angle 0.69884 / 0.34 (21722) hydrogen bonds : bond 0.04429 / 3.02 ( 716) hydrogen bonds : angle 4.92391 / 3.52 ( 2059) Misc. bond : bond 0.00025 / 0.01 ( 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 185 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.451 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: 0.4079 (mpp) cc_final: 0.3544 (mmt) REVERT: A 560 MET cc_start: 0.4759 (mmp) cc_final: 0.4472 (mmp) REVERT: A 1609 MET cc_start: 0.5391 (tpp) cc_final: 0.5135 (tpp) REVERT: A 2151 MET cc_start: 0.7021 (mpp) cc_final: 0.6766 (mpp) REVERT: A 2163 MET cc_start: 0.6936 (mpp) cc_final: 0.6634 (mmt) outliers start: 19 outliers final: 13 residues processed: 176 average time/residue: 0.1101 time to fit residues: 30.3501 Evaluate side-chains 137 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 0.6980 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS A 341 HIS A 770 GLN A 787 ASN A1620 ASN A1668 ASN ** K 438 HIS ** 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 = 0.4840 r_free = 0.4840 target = 0.164732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.137717 restraints weight = 43349.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.137011 restraints weight = 42003.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.138655 restraints weight = 34043.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.139267 restraints weight = 23678.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.139690 restraints weight = 22883.403| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15894 Z= 0.203 Angle : 0.736 12.067 21722 Z= 0.364 Chirality : 0.048 0.401 2459 Planarity : 0.005 0.062 2656 Dihedral : 8.698 72.125 2475 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.73 % Favored : 92.93 % Rotamer: Outliers : 2.36 % Allowed : 11.50 % Favored : 86.13 % 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: -1.01 (0.19), residues: 1783 helix: 0.16 (0.17), residues: 835 sheet: -0.83 (0.40), residues: 172 loop : -1.51 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.017 0.002 TYR A2115 PHE 0.021 0.002 PHE K 367 TRP 0.029 0.003 TRP A 848 HIS 0.017 0.002 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (15893) covalent geometry : angle 0.73566 / 0.36 (21722) hydrogen bonds : bond 0.04776 / 3.29 ( 716) hydrogen bonds : angle 4.96213 / 3.55 ( 2059) Misc. bond : bond 0.00010 / 0.01 ( 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 181 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.567 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: 0.6141 (mpp) cc_final: 0.5489 (tpp) REVERT: A 108 TRP cc_start: 0.4930 (m-10) cc_final: 0.4706 (m-10) REVERT: A 161 MET cc_start: 0.3992 (mpp) cc_final: 0.3509 (mmt) REVERT: A 560 MET cc_start: 0.4916 (mmp) cc_final: 0.4639 (mmp) REVERT: A 1112 MET cc_start: 0.6237 (tpt) cc_final: 0.5873 (tpt) REVERT: A 1202 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6945 (t0) REVERT: A 1664 PHE cc_start: 0.5185 (OUTLIER) cc_final: 0.4348 (m-10) REVERT: A 2151 MET cc_start: 0.7068 (mpp) cc_final: 0.6727 (mpp) REVERT: K 368 HIS cc_start: 0.1614 (m-70) cc_final: 0.1304 (m-70) outliers start: 38 outliers final: 24 residues processed: 167 average time/residue: 0.1055 time to fit residues: 27.6908 Evaluate side-chains 147 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 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 880 LEU Chi-restraints excluded: chain A residue 1031 VAL 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 1796 GLU Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 1959 GLU 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 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: 6.9990 chunk 115 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 0.0470 chunk 140 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 318 HIS A 341 HIS A 787 ASN A1833 HIS A1896 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.166407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.140384 restraints weight = 42959.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.141043 restraints weight = 41229.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.141877 restraints weight = 34922.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.142309 restraints weight = 22371.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.142900 restraints weight = 20466.197| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15894 Z= 0.151 Angle : 0.671 8.473 21722 Z= 0.329 Chirality : 0.046 0.365 2459 Planarity : 0.005 0.062 2656 Dihedral : 8.444 72.571 2475 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.83 % Favored : 93.83 % Rotamer: Outliers : 2.18 % Allowed : 13.87 % Favored : 83.96 % 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: -0.71 (0.20), residues: 1783 helix: 0.43 (0.17), residues: 834 sheet: -0.60 (0.40), residues: 167 loop : -1.40 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.016 0.002 TYR A1890 PHE 0.019 0.002 PHE A1552 TRP 0.029 0.002 TRP A1834 HIS 0.021 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (15893) covalent geometry : angle 0.67082 / 0.33 (21722) hydrogen bonds : bond 0.04238 / 2.92 ( 716) hydrogen bonds : angle 4.71690 / 3.37 ( 2059) Misc. bond : bond 0.00009 / 0.00 ( 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 176 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7196 (m) cc_final: 0.6950 (m) REVERT: A 161 MET cc_start: 0.3757 (mpp) cc_final: 0.3167 (mmt) REVERT: A 178 LEU cc_start: 0.6987 (mt) cc_final: 0.6429 (mp) REVERT: A 560 MET cc_start: 0.4992 (mmp) cc_final: 0.4637 (mmp) REVERT: A 935 GLU cc_start: 0.6614 (tt0) cc_final: 0.5940 (tt0) REVERT: A 1112 MET cc_start: 0.6308 (tpt) cc_final: 0.5938 (tpt) REVERT: A 1594 LYS cc_start: 0.6181 (pttm) cc_final: 0.5927 (pttt) REVERT: A 1609 MET cc_start: 0.6209 (tpp) cc_final: 0.5663 (tpp) REVERT: A 1664 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4286 (m-10) REVERT: A 1959 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: A 2151 MET cc_start: 0.6947 (mpp) cc_final: 0.6599 (mpp) REVERT: K 368 HIS cc_start: 0.1797 (m-70) cc_final: 0.1456 (m-70) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.1022 time to fit residues: 26.9715 Evaluate side-chains 150 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 1662 ASP 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 1796 GLU Chi-restraints excluded: chain A residue 1959 GLU 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 K residue 172 SER Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 76 optimal weight: 0.0050 chunk 51 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 341 HIS A 787 ASN ** K 438 HIS ** 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 = 0.4861 r_free = 0.4861 target = 0.165880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.139948 restraints weight = 43013.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.139193 restraints weight = 42225.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.140591 restraints weight = 35058.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.141105 restraints weight = 23212.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.141417 restraints weight = 22776.476| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15894 Z= 0.158 Angle : 0.668 9.106 21722 Z= 0.329 Chirality : 0.046 0.356 2459 Planarity : 0.004 0.063 2656 Dihedral : 8.355 72.757 2475 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.17 % Favored : 93.49 % Rotamer: Outliers : 2.49 % Allowed : 16.17 % Favored : 81.34 % 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: -0.58 (0.20), residues: 1783 helix: 0.65 (0.17), residues: 827 sheet: -0.84 (0.39), residues: 179 loop : -1.37 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2181 TYR 0.024 0.002 TYR A1148 PHE 0.019 0.002 PHE K 367 TRP 0.028 0.002 TRP A1834 HIS 0.019 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (15893) covalent geometry : angle 0.66839 / 0.33 (21722) hydrogen bonds : bond 0.04193 / 2.90 ( 716) hydrogen bonds : angle 4.70992 / 3.37 ( 2059) Misc. bond : bond 0.00008 / 0.00 ( 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 176 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7152 (m) cc_final: 0.6917 (m) REVERT: A 84 MET cc_start: 0.6048 (mpp) cc_final: 0.5779 (mpp) REVERT: A 161 MET cc_start: 0.3778 (mpp) cc_final: 0.3300 (mmt) REVERT: A 560 MET cc_start: 0.4991 (mmp) cc_final: 0.4680 (mmp) REVERT: A 900 LEU cc_start: 0.6528 (mt) cc_final: 0.6243 (mt) REVERT: A 1112 MET cc_start: 0.6400 (tpt) cc_final: 0.5943 (tpt) REVERT: A 1594 LYS cc_start: 0.6237 (pttm) cc_final: 0.6012 (pttt) REVERT: A 1664 PHE cc_start: 0.5127 (OUTLIER) cc_final: 0.4393 (m-10) REVERT: A 2151 MET cc_start: 0.6907 (mpp) cc_final: 0.6587 (mpp) REVERT: K 164 GLU cc_start: 0.3538 (OUTLIER) cc_final: 0.3153 (pp20) REVERT: K 368 HIS cc_start: 0.1735 (m-70) cc_final: 0.1473 (m-70) outliers start: 40 outliers final: 31 residues processed: 160 average time/residue: 0.1029 time to fit residues: 26.1819 Evaluate side-chains 162 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 864 THR 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 1662 ASP 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 1796 GLU 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 2117 LEU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 172 SER 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: 0.9980 chunk 100 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 61 optimal weight: 0.0270 chunk 122 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 HIS A1080 ASN A1543 GLN A2223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.168088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.142563 restraints weight = 42918.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.141700 restraints weight = 40725.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.143367 restraints weight = 32706.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.143864 restraints weight = 21780.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144226 restraints weight = 21459.657| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15894 Z= 0.120 Angle : 0.623 12.053 21722 Z= 0.306 Chirality : 0.044 0.345 2459 Planarity : 0.004 0.062 2656 Dihedral : 8.152 72.491 2475 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 2.24 % Allowed : 17.04 % Favored : 80.72 % 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: -0.30 (0.20), residues: 1783 helix: 0.95 (0.18), residues: 832 sheet: -0.92 (0.38), residues: 184 loop : -1.28 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2222 TYR 0.027 0.001 TYR A1148 PHE 0.019 0.001 PHE K 367 TRP 0.032 0.002 TRP A1834 HIS 0.016 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15893) covalent geometry : angle 0.62348 / 0.31 (21722) hydrogen bonds : bond 0.03727 / 2.59 ( 716) hydrogen bonds : angle 4.43816 / 3.17 ( 2059) Misc. bond : bond 0.00014 / 0.01 ( 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 173 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.581 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: 0.6916 (m) cc_final: 0.6639 (m) REVERT: A 84 MET cc_start: 0.6030 (mpp) cc_final: 0.5549 (tpp) REVERT: A 100 MET cc_start: 0.6165 (tpp) cc_final: 0.5914 (tmm) REVERT: A 108 TRP cc_start: 0.4732 (m-90) cc_final: 0.4335 (m-10) REVERT: A 161 MET cc_start: 0.3699 (mpp) cc_final: 0.3293 (mmt) REVERT: A 560 MET cc_start: 0.4952 (mmp) cc_final: 0.4620 (mmp) REVERT: A 1037 LEU cc_start: 0.5675 (mp) cc_final: 0.4965 (pp) REVERT: A 1112 MET cc_start: 0.6451 (tpt) cc_final: 0.5982 (tpt) REVERT: A 1593 LEU cc_start: 0.0814 (OUTLIER) cc_final: -0.0111 (mt) REVERT: A 1664 PHE cc_start: 0.4893 (OUTLIER) cc_final: 0.4157 (m-10) REVERT: A 2151 MET cc_start: 0.6903 (mpp) cc_final: 0.6571 (mpp) REVERT: K 164 GLU cc_start: 0.3394 (OUTLIER) cc_final: 0.2997 (pp20) REVERT: K 359 GLN cc_start: 0.7494 (tt0) cc_final: 0.6894 (pt0) outliers start: 36 outliers final: 23 residues processed: 158 average time/residue: 0.1032 time to fit residues: 25.7438 Evaluate side-chains 151 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1544 GLN 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 1796 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 78 optimal weight: 0.9990 chunk 169 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 HIS ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.166434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.140379 restraints weight = 42781.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.139773 restraints weight = 41471.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.141310 restraints weight = 32488.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.141681 restraints weight = 21783.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.141951 restraints weight = 21904.690| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15894 Z= 0.146 Angle : 0.663 14.686 21722 Z= 0.322 Chirality : 0.045 0.368 2459 Planarity : 0.004 0.061 2656 Dihedral : 8.158 72.823 2475 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.28 % Favored : 93.44 % Rotamer: Outliers : 2.43 % Allowed : 17.54 % 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: -0.27 (0.20), residues: 1783 helix: 1.00 (0.18), residues: 824 sheet: -0.94 (0.38), residues: 188 loop : -1.26 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2222 TYR 0.032 0.002 TYR A1148 PHE 0.023 0.002 PHE A 15 TRP 0.029 0.002 TRP A1834 HIS 0.015 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15893) covalent geometry : angle 0.66259 / 0.32 (21722) hydrogen bonds : bond 0.03960 / 2.75 ( 716) hydrogen bonds : angle 4.51862 / 3.23 ( 2059) Misc. bond : bond 0.00003 / 0.00 ( 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 173 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.516 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: 0.7018 (m) cc_final: 0.6745 (m) REVERT: A 84 MET cc_start: 0.6022 (mpp) cc_final: 0.5614 (tpp) REVERT: A 161 MET cc_start: 0.3763 (mpp) cc_final: 0.3143 (mmt) REVERT: A 560 MET cc_start: 0.5234 (mmp) cc_final: 0.4905 (mmp) REVERT: A 1112 MET cc_start: 0.6456 (tpt) cc_final: 0.5870 (tpt) REVERT: A 1593 LEU cc_start: 0.0640 (OUTLIER) cc_final: -0.0338 (mt) REVERT: A 1664 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.4298 (m-10) REVERT: A 2151 MET cc_start: 0.6934 (mpp) cc_final: 0.6594 (mpp) REVERT: K 164 GLU cc_start: 0.3392 (OUTLIER) cc_final: 0.2995 (pp20) REVERT: K 359 GLN cc_start: 0.7633 (tt0) cc_final: 0.6951 (pt0) outliers start: 39 outliers final: 28 residues processed: 159 average time/residue: 0.0986 time to fit residues: 24.9301 Evaluate side-chains 162 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 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 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 864 THR 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 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN 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 1796 GLU 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 K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL 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: 4.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1202 ASN A1543 GLN A2053 GLN ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.166627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.139859 restraints weight = 43048.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.139615 restraints weight = 37514.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.140826 restraints weight = 30500.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.141549 restraints weight = 20875.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.141729 restraints weight = 20546.550| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15894 Z= 0.131 Angle : 0.655 12.330 21722 Z= 0.318 Chirality : 0.045 0.365 2459 Planarity : 0.004 0.061 2656 Dihedral : 8.101 72.835 2475 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 2.86 % Allowed : 17.72 % Favored : 79.42 % 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: -0.23 (0.20), residues: 1783 helix: 1.04 (0.18), residues: 832 sheet: -0.84 (0.39), residues: 183 loop : -1.30 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.031 0.002 TYR A1148 PHE 0.024 0.001 PHE A 343 TRP 0.032 0.002 TRP A1834 HIS 0.014 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15893) covalent geometry : angle 0.65458 / 0.32 (21722) hydrogen bonds : bond 0.03770 / 2.63 ( 716) hydrogen bonds : angle 4.45561 / 3.18 ( 2059) Misc. bond : bond 0.00011 / 0.01 ( 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 189 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7041 (m) cc_final: 0.6673 (m) REVERT: A 84 MET cc_start: 0.6054 (mpp) cc_final: 0.5710 (tpp) REVERT: A 161 MET cc_start: 0.3743 (mpp) cc_final: 0.3098 (mmt) REVERT: A 1593 LEU cc_start: 0.0667 (OUTLIER) cc_final: -0.0321 (mt) REVERT: A 1664 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.4290 (m-10) REVERT: A 2151 MET cc_start: 0.6954 (mpp) cc_final: 0.6553 (mpp) REVERT: K 164 GLU cc_start: 0.3253 (OUTLIER) cc_final: 0.2829 (pp20) REVERT: K 359 GLN cc_start: 0.7450 (tt0) cc_final: 0.6729 (pt0) outliers start: 46 outliers final: 32 residues processed: 173 average time/residue: 0.1005 time to fit residues: 27.9063 Evaluate side-chains 163 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 864 THR 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 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN 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 1796 GLU 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 2053 GLN 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 436 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 6 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 111 optimal weight: 0.0060 chunk 90 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1147 GLN A1543 GLN A2053 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.167554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.140929 restraints weight = 42819.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.140506 restraints weight = 36642.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.141650 restraints weight = 29910.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.142097 restraints weight = 20230.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142345 restraints weight = 19693.146| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.3464 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= 0.119 Angle : 0.654 12.041 21722 Z= 0.319 Chirality : 0.045 0.357 2459 Planarity : 0.005 0.099 2656 Dihedral : 8.049 72.592 2475 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.89 % Favored : 93.83 % Rotamer: Outliers : 2.67 % Allowed : 18.35 % Favored : 78.98 % 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: -0.13 (0.20), residues: 1783 helix: 1.13 (0.18), residues: 833 sheet: -0.83 (0.39), residues: 181 loop : -1.24 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 602 TYR 0.031 0.001 TYR A1148 PHE 0.026 0.001 PHE K 367 TRP 0.031 0.002 TRP A1834 HIS 0.014 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15893) covalent geometry : angle 0.65402 / 0.32 (21722) hydrogen bonds : bond 0.03662 / 2.55 ( 716) hydrogen bonds : angle 4.39778 / 3.15 ( 2059) Misc. bond : bond 0.00013 / 0.01 ( 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 170 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6971 (m) cc_final: 0.6120 (m) REVERT: A 63 ARG cc_start: 0.3268 (mmp-170) cc_final: 0.2453 (mmp80) REVERT: A 84 MET cc_start: 0.5991 (mpp) cc_final: 0.5639 (tpp) REVERT: A 161 MET cc_start: 0.3694 (mpp) cc_final: 0.3036 (mmt) REVERT: A 338 LEU cc_start: 0.7464 (tp) cc_final: 0.7139 (pp) REVERT: A 863 TYR cc_start: 0.4543 (OUTLIER) cc_final: 0.4004 (t80) REVERT: A 1593 LEU cc_start: 0.0592 (OUTLIER) cc_final: -0.0384 (mt) REVERT: A 1664 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.4139 (m-10) REVERT: A 2014 MET cc_start: 0.6666 (mmm) cc_final: 0.6350 (mmm) REVERT: A 2151 MET cc_start: 0.6868 (mpp) cc_final: 0.6505 (mpp) REVERT: K 164 GLU cc_start: 0.3224 (OUTLIER) cc_final: 0.2807 (pp20) REVERT: K 359 GLN cc_start: 0.7486 (tt0) cc_final: 0.6836 (pt0) outliers start: 43 outliers final: 34 residues processed: 154 average time/residue: 0.1039 time to fit residues: 25.8810 Evaluate side-chains 157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 203 ILE 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 864 THR 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 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN 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 1796 GLU 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 2104 GLN 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 405 ASN Chi-restraints excluded: chain K residue 436 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN A2053 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.166830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.140129 restraints weight = 42760.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.139652 restraints weight = 36415.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.140942 restraints weight = 29879.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.141426 restraints weight = 20711.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.141656 restraints weight = 20430.102| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15894 Z= 0.130 Angle : 0.661 11.830 21722 Z= 0.321 Chirality : 0.044 0.366 2459 Planarity : 0.005 0.077 2656 Dihedral : 8.037 72.676 2475 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.00 % Favored : 93.72 % Rotamer: Outliers : 2.55 % Allowed : 18.66 % Favored : 78.79 % 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: -0.15 (0.20), residues: 1783 helix: 1.08 (0.18), residues: 837 sheet: -0.83 (0.39), residues: 181 loop : -1.23 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 170 TYR 0.029 0.001 TYR A1148 PHE 0.027 0.001 PHE K 367 TRP 0.031 0.002 TRP A1834 HIS 0.015 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15893) covalent geometry : angle 0.66071 / 0.32 (21722) hydrogen bonds : bond 0.03696 / 2.57 ( 716) hydrogen bonds : angle 4.42653 / 3.17 ( 2059) Misc. bond : bond 0.00008 / 0.00 ( 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 164 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.3211 (mmp-170) cc_final: 0.2453 (mmp80) REVERT: A 84 MET cc_start: 0.6043 (mpp) cc_final: 0.5699 (tpp) REVERT: A 161 MET cc_start: 0.3803 (mpp) cc_final: 0.3144 (mmt) REVERT: A 338 LEU cc_start: 0.7518 (tp) cc_final: 0.7226 (pp) REVERT: A 863 TYR cc_start: 0.4483 (OUTLIER) cc_final: 0.4004 (t80) REVERT: A 1593 LEU cc_start: 0.0613 (OUTLIER) cc_final: -0.0384 (mt) REVERT: A 1664 PHE cc_start: 0.4847 (OUTLIER) cc_final: 0.4156 (m-10) REVERT: A 2117 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.3409 (tp) REVERT: A 2151 MET cc_start: 0.6879 (mpp) cc_final: 0.6493 (mpp) REVERT: K 164 GLU cc_start: 0.3250 (OUTLIER) cc_final: 0.2822 (pp20) REVERT: K 359 GLN cc_start: 0.7402 (tt0) cc_final: 0.6723 (pt0) outliers start: 41 outliers final: 34 residues processed: 147 average time/residue: 0.1049 time to fit residues: 24.5181 Evaluate side-chains 156 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 203 ILE 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 864 THR 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 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN 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 1796 GLU 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 2053 GLN Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2104 GLN 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 405 ASN Chi-restraints excluded: chain K residue 436 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 86 optimal weight: 0.1980 chunk 50 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN A2053 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.168238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.141731 restraints weight = 42758.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.142035 restraints weight = 33176.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.143370 restraints weight = 27622.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.143410 restraints weight = 19195.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.143828 restraints weight = 19032.641| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15894 Z= 0.114 Angle : 0.661 12.907 21722 Z= 0.318 Chirality : 0.044 0.352 2459 Planarity : 0.004 0.060 2656 Dihedral : 7.971 72.380 2475 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.55 % Favored : 94.17 % Rotamer: Outliers : 2.30 % Allowed : 19.28 % Favored : 78.42 % 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: -0.04 (0.21), residues: 1783 helix: 1.21 (0.18), residues: 833 sheet: -0.77 (0.40), residues: 181 loop : -1.22 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2052 TYR 0.034 0.001 TYR A1148 PHE 0.026 0.001 PHE K 367 TRP 0.030 0.002 TRP A1834 HIS 0.015 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15893) covalent geometry : angle 0.66149 / 0.32 (21722) hydrogen bonds : bond 0.03533 / 2.46 ( 716) hydrogen bonds : angle 4.34830 / 3.11 ( 2059) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.46 seconds wall clock time: 45 minutes 20.27 seconds (2720.27 seconds total)