Starting phenix.real_space_refine on Sat Jun 14 10:15:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dga_27420/06_2025/8dga_27420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dga_27420/06_2025/8dga_27420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dga_27420/06_2025/8dga_27420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dga_27420/06_2025/8dga_27420.map" model { file = "/net/cci-nas-00/data/ceres_data/8dga_27420/06_2025/8dga_27420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dga_27420/06_2025/8dga_27420.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15473 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1629, 13162 Classifications: {'peptide': 1629} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 1532} Chain breaks: 11 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 414 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 16} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1424 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 10.29, per 1000 atoms: 0.67 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: 4.07 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 5.39 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: 7.86 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3969 1.33 - 1.46: 3438 1.46 - 1.58: 8294 1.58 - 1.70: 83 1.70 - 1.82: 109 Bond restraints: 15893 Sorted by residual: bond pdb=" O5' U5P E 101 " pdb=" P U5P E 101 " ideal model delta sigma weight residual 1.711 1.590 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C GLU A 931 " pdb=" N PRO A 932 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.38e-02 5.25e+03 6.95e+00 bond pdb=" CG LEU A1915 " pdb=" CD1 LEU A1915 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.70e+00 bond pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " ideal model delta sigma weight residual 1.520 1.591 -0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" CG LEU A2147 " pdb=" CD1 LEU A2147 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.52e+00 ... (remaining 15888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 21231 3.37 - 6.75: 418 6.75 - 10.12: 58 10.12 - 13.50: 14 13.50 - 16.87: 1 Bond angle restraints: 21722 Sorted by residual: angle pdb=" C ARG A 866 " pdb=" N LEU A 867 " pdb=" CA LEU A 867 " ideal model delta sigma weight residual 121.03 129.62 -8.59 1.60e+00 3.91e-01 2.88e+01 angle pdb=" C CYS A 107 " pdb=" N TRP A 108 " pdb=" CA TRP A 108 " ideal model delta sigma weight residual 120.72 129.39 -8.67 1.67e+00 3.59e-01 2.69e+01 angle pdb=" N GLU A 196 " pdb=" CA GLU A 196 " pdb=" CB GLU A 196 " ideal model delta sigma weight residual 110.16 117.75 -7.59 1.48e+00 4.57e-01 2.63e+01 angle pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " pdb=" CD GLN A2053 " ideal model delta sigma weight residual 112.60 121.05 -8.45 1.70e+00 3.46e-01 2.47e+01 angle pdb=" N ASP A2123 " pdb=" CA ASP A2123 " pdb=" C ASP A2123 " ideal model delta sigma weight residual 112.92 106.96 5.96 1.23e+00 6.61e-01 2.35e+01 ... (remaining 21717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8735 17.90 - 35.80: 782 35.80 - 53.70: 149 53.70 - 71.59: 61 71.59 - 89.49: 17 Dihedral angle restraints: 9744 sinusoidal: 4419 harmonic: 5325 Sorted by residual: dihedral pdb=" CA VAL A 14 " pdb=" C VAL A 14 " pdb=" N PHE A 15 " pdb=" CA PHE A 15 " ideal model delta harmonic sigma weight residual -180.00 -119.71 -60.29 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LEU A2117 " pdb=" C LEU A2117 " pdb=" N SER A2118 " pdb=" CA SER A2118 " ideal model delta harmonic sigma weight residual 180.00 132.42 47.58 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA ILE A1829 " pdb=" C ILE A1829 " pdb=" N PRO A1830 " pdb=" CA PRO A1830 " ideal model delta harmonic sigma weight residual 180.00 145.26 34.74 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2253 0.105 - 0.211: 186 0.211 - 0.316: 15 0.316 - 0.421: 3 0.421 - 0.527: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CG LEU A 496 " pdb=" CB LEU A 496 " pdb=" CD1 LEU A 496 " pdb=" CD2 LEU A 496 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CB ILE A1829 " pdb=" CA ILE A1829 " pdb=" CG1 ILE A1829 " pdb=" CG2 ILE A1829 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE A1010 " pdb=" CA ILE A1010 " pdb=" CG1 ILE A1010 " pdb=" CG2 ILE A1010 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2456 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 108 " 0.058 2.00e-02 2.50e+03 6.16e-02 9.49e+01 pdb=" CG TRP A 108 " -0.154 2.00e-02 2.50e+03 pdb=" CD1 TRP A 108 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TRP A 108 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 108 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 108 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 108 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 108 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 108 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 848 " -0.032 2.00e-02 2.50e+03 4.46e-02 4.97e+01 pdb=" CG TRP A 848 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 848 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP A 848 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 848 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 848 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 848 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 848 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 848 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 848 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A2053 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN A2053 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN A2053 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A2054 " 0.021 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1725 2.75 - 3.29: 15109 3.29 - 3.82: 27254 3.82 - 4.36: 31780 4.36 - 4.90: 51164 Nonbonded interactions: 127032 Sorted by model distance: nonbonded pdb=" O ARG A1207 " pdb=" O2' A F 50 " model vdw 2.210 3.040 nonbonded pdb=" O LEU K 459 " pdb=" OG1 THR K 463 " model vdw 2.264 3.040 nonbonded pdb=" O PHE A 841 " pdb=" OG SER A2089 " model vdw 2.266 3.040 nonbonded pdb=" O VAL A1767 " pdb=" NH1 ARG A2030 " model vdw 2.283 3.120 nonbonded pdb=" O GLY A 294 " pdb=" OG1 THR A 298 " model vdw 2.283 3.040 ... (remaining 127027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 137.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.710 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 15894 Z= 0.316 Angle : 1.166 16.872 21722 Z= 0.598 Chirality : 0.062 0.527 2459 Planarity : 0.009 0.121 2656 Dihedral : 15.030 89.493 6284 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (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 TRP 0.154 0.009 TRP A 108 HIS 0.014 0.002 HIS A1196 PHE 0.047 0.004 PHE A 15 TYR 0.031 0.004 TYR A1175 ARG 0.023 0.001 ARG A2045 Details of bonding type rmsd hydrogen bonds : bond 0.14567 ( 716) hydrogen bonds : angle 6.89311 ( 2059) covalent geometry : bond 0.00721 (15893) covalent geometry : angle 1.16602 (21722) Misc. bond : bond 0.04738 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 1.803 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: 0.3189 time to fit residues: 87.0841 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 : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 93 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS A 770 GLN A 885 GLN A1189 GLN A1620 ASN A2016 HIS K 163 HIS K 405 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.170228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.144035 restraints weight = 42813.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.143102 restraints weight = 37317.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.144858 restraints weight = 28972.297| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15894 Z= 0.137 Angle : 0.666 14.788 21722 Z= 0.339 Chirality : 0.042 0.239 2459 Planarity : 0.005 0.061 2656 Dihedral : 12.664 96.720 2633 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.55 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 7.28 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.19), residues: 1783 helix: -0.11 (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 TRP 0.046 0.003 TRP A 108 HIS 0.006 0.001 HIS K 368 PHE 0.022 0.002 PHE A1552 TYR 0.023 0.002 TYR K 458 ARG 0.008 0.001 ARG A 775 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 716) hydrogen bonds : angle 4.98572 ( 2059) covalent geometry : bond 0.00295 (15893) covalent geometry : angle 0.66574 (21722) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.3996 (mpp) cc_final: 0.3465 (mmt) REVERT: A 560 MET cc_start: 0.4604 (mmp) cc_final: 0.4294 (mmp) REVERT: A 2151 MET cc_start: 0.7023 (mpp) cc_final: 0.6791 (mpp) REVERT: A 2163 MET cc_start: 0.6955 (mpp) cc_final: 0.6661 (mmt) outliers start: 20 outliers final: 13 residues processed: 173 average time/residue: 0.2556 time to fit residues: 68.4290 Evaluate side-chains 138 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 143 optimal weight: 1.9990 chunk 169 optimal weight: 0.0470 chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS A 787 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.167754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.141562 restraints weight = 42898.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.141012 restraints weight = 39148.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.142166 restraints weight = 32350.833| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15894 Z= 0.150 Angle : 0.642 11.840 21722 Z= 0.327 Chirality : 0.042 0.207 2459 Planarity : 0.005 0.066 2656 Dihedral : 12.201 96.296 2633 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.11 % Favored : 93.55 % Rotamer: Outliers : 1.87 % Allowed : 11.01 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1783 helix: 0.33 (0.17), residues: 837 sheet: -0.76 (0.40), residues: 172 loop : -1.44 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 108 HIS 0.012 0.001 HIS K 194 PHE 0.020 0.002 PHE K 367 TYR 0.018 0.002 TYR A1148 ARG 0.004 0.000 ARG A2181 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 716) hydrogen bonds : angle 4.76715 ( 2059) covalent geometry : bond 0.00338 (15893) covalent geometry : angle 0.64216 (21722) Misc. bond : bond 0.00039 ( 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 177 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.812 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: 0.6132 (mpp) cc_final: 0.5479 (tpp) REVERT: A 108 TRP cc_start: 0.4720 (m-10) cc_final: 0.4492 (m-10) REVERT: A 560 MET cc_start: 0.4698 (mmp) cc_final: 0.4403 (mmp) REVERT: A 1112 MET cc_start: 0.6136 (tpt) cc_final: 0.5901 (tpt) REVERT: A 2151 MET cc_start: 0.7004 (mpp) cc_final: 0.6700 (mpp) REVERT: A 2163 MET cc_start: 0.6995 (mpp) cc_final: 0.6658 (mmt) REVERT: K 368 HIS cc_start: 0.1649 (m-70) cc_final: 0.1407 (m-70) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.3246 time to fit residues: 85.3414 Evaluate side-chains 150 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 423 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 341 HIS A 787 ASN A 885 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 ASN ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1833 HIS A1981 ASN K 454 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.163009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.137432 restraints weight = 42825.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.140621 restraints weight = 42951.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.140474 restraints weight = 31519.580| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15894 Z= 0.216 Angle : 0.724 10.458 21722 Z= 0.369 Chirality : 0.044 0.212 2459 Planarity : 0.005 0.080 2656 Dihedral : 12.169 94.057 2633 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.01 % Favored : 92.65 % Rotamer: Outliers : 2.67 % Allowed : 13.56 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1783 helix: 0.29 (0.17), residues: 824 sheet: -0.71 (0.40), residues: 172 loop : -1.52 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 848 HIS 0.019 0.002 HIS K 194 PHE 0.021 0.002 PHE A 15 TYR 0.015 0.002 TYR A1797 ARG 0.006 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 716) hydrogen bonds : angle 5.01121 ( 2059) covalent geometry : bond 0.00495 (15893) covalent geometry : angle 0.72363 (21722) Misc. bond : bond 0.00049 ( 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 188 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7011 (mt) cc_final: 0.6802 (mp) REVERT: A 560 MET cc_start: 0.5021 (mmp) cc_final: 0.4706 (mmp) REVERT: A 900 LEU cc_start: 0.6447 (mt) cc_final: 0.6236 (mt) REVERT: A 935 GLU cc_start: 0.6612 (tt0) cc_final: 0.5883 (tt0) REVERT: A 1112 MET cc_start: 0.6380 (tpt) cc_final: 0.6030 (tpt) REVERT: A 1202 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.6978 (t0) REVERT: A 1664 PHE cc_start: 0.5336 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: A 2151 MET cc_start: 0.7037 (mpp) cc_final: 0.6604 (mpp) REVERT: K 368 HIS cc_start: 0.1892 (m-70) cc_final: 0.1478 (m-70) outliers start: 43 outliers final: 33 residues processed: 170 average time/residue: 0.3174 time to fit residues: 84.4408 Evaluate side-chains 162 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 15 PHE Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR 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 2149 SER Chi-restraints excluded: chain A residue 2159 VAL 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 8 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 31 optimal weight: 0.0370 chunk 124 optimal weight: 0.0270 chunk 165 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 787 ASN A 885 GLN A1080 ASN A1544 GLN A1736 ASN A1896 HIS A2223 ASN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.168315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.141855 restraints weight = 43119.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.141987 restraints weight = 34649.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.143208 restraints weight = 30285.961| |-----------------------------------------------------------------------------| r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15894 Z= 0.118 Angle : 0.602 8.104 21722 Z= 0.308 Chirality : 0.041 0.207 2459 Planarity : 0.004 0.063 2656 Dihedral : 11.808 98.182 2633 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.22 % Favored : 94.45 % Rotamer: Outliers : 1.49 % Allowed : 16.79 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1783 helix: 0.80 (0.18), residues: 831 sheet: -0.96 (0.38), residues: 189 loop : -1.25 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 108 HIS 0.007 0.001 HIS K 194 PHE 0.019 0.001 PHE K 367 TYR 0.025 0.001 TYR A1148 ARG 0.006 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 716) hydrogen bonds : angle 4.52528 ( 2059) covalent geometry : bond 0.00255 (15893) covalent geometry : angle 0.60218 (21722) Misc. bond : bond 0.00032 ( 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 165 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7020 (m) cc_final: 0.6758 (m) REVERT: A 108 TRP cc_start: 0.4851 (m-90) cc_final: 0.4461 (m-10) REVERT: A 560 MET cc_start: 0.5002 (mmp) cc_final: 0.4673 (mmp) REVERT: A 1112 MET cc_start: 0.6469 (tpt) cc_final: 0.6178 (tpt) REVERT: A 1593 LEU cc_start: 0.0770 (OUTLIER) cc_final: -0.0127 (mt) REVERT: A 1664 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.4282 (m-10) REVERT: A 1929 TRP cc_start: 0.7410 (t60) cc_final: 0.6836 (t60) REVERT: A 2151 MET cc_start: 0.6896 (mpp) cc_final: 0.6634 (mpp) REVERT: K 164 GLU cc_start: 0.3415 (OUTLIER) cc_final: 0.3038 (pp20) REVERT: K 368 HIS cc_start: 0.1862 (m-70) cc_final: 0.1627 (m-70) outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 0.2669 time to fit residues: 65.6980 Evaluate side-chains 144 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 0.3980 chunk 64 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 175 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.167910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.141273 restraints weight = 42971.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.140906 restraints weight = 35610.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.142116 restraints weight = 27764.783| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15894 Z= 0.118 Angle : 0.604 15.167 21722 Z= 0.304 Chirality : 0.041 0.203 2459 Planarity : 0.004 0.058 2656 Dihedral : 11.643 96.054 2633 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 2.24 % Allowed : 17.10 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1783 helix: 0.94 (0.18), residues: 836 sheet: -0.87 (0.38), residues: 188 loop : -1.23 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 848 HIS 0.006 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.024 0.001 TYR A1148 ARG 0.005 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 716) hydrogen bonds : angle 4.45070 ( 2059) covalent geometry : bond 0.00260 (15893) covalent geometry : angle 0.60409 (21722) Misc. bond : bond 0.00028 ( 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 : 1.730 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: symmetry clash REVERT: A 33 THR cc_start: 0.7093 (m) cc_final: 0.6822 (m) REVERT: A 84 MET cc_start: 0.6013 (mpp) cc_final: 0.5738 (mpp) REVERT: A 108 TRP cc_start: 0.4938 (m-90) cc_final: 0.4509 (m-10) REVERT: A 560 MET cc_start: 0.5008 (mmp) cc_final: 0.4681 (mmp) REVERT: A 1112 MET cc_start: 0.6440 (tpt) cc_final: 0.6105 (tpt) REVERT: A 1593 LEU cc_start: 0.0695 (OUTLIER) cc_final: -0.0254 (mt) REVERT: A 1664 PHE cc_start: 0.5008 (OUTLIER) cc_final: 0.4240 (m-10) REVERT: A 2151 MET cc_start: 0.6886 (mpp) cc_final: 0.6552 (mpp) REVERT: K 164 GLU cc_start: 0.3295 (OUTLIER) cc_final: 0.2908 (pp20) outliers start: 36 outliers final: 22 residues processed: 163 average time/residue: 0.2753 time to fit residues: 68.6006 Evaluate side-chains 150 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 174 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1543 GLN ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.166139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.140388 restraints weight = 42944.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.141214 restraints weight = 38684.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142221 restraints weight = 31126.721| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15894 Z= 0.146 Angle : 0.632 13.501 21722 Z= 0.319 Chirality : 0.042 0.203 2459 Planarity : 0.004 0.058 2656 Dihedral : 11.677 94.560 2633 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 2.24 % Allowed : 17.79 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1783 helix: 0.96 (0.18), residues: 836 sheet: -0.79 (0.39), residues: 183 loop : -1.27 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1834 HIS 0.009 0.001 HIS K 368 PHE 0.023 0.002 PHE A1554 TYR 0.033 0.002 TYR A1148 ARG 0.004 0.000 ARG A2222 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 716) hydrogen bonds : angle 4.51306 ( 2059) covalent geometry : bond 0.00333 (15893) covalent geometry : angle 0.63221 (21722) Misc. bond : bond 0.00020 ( 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 170 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.614 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: 0.7072 (m) cc_final: 0.6807 (m) REVERT: A 100 MET cc_start: 0.6419 (tpp) cc_final: 0.6175 (tmm) REVERT: A 338 LEU cc_start: 0.7366 (tp) cc_final: 0.7087 (pp) REVERT: A 560 MET cc_start: 0.5211 (mmp) cc_final: 0.4864 (mmp) REVERT: A 1112 MET cc_start: 0.6505 (tpt) cc_final: 0.6142 (tpt) REVERT: A 1593 LEU cc_start: 0.0581 (OUTLIER) cc_final: -0.0392 (mt) REVERT: A 1664 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.4280 (m-10) REVERT: A 2151 MET cc_start: 0.6968 (mpp) cc_final: 0.6576 (mpp) REVERT: K 164 GLU cc_start: 0.3319 (OUTLIER) cc_final: 0.2893 (pp20) outliers start: 36 outliers final: 25 residues processed: 158 average time/residue: 0.2547 time to fit residues: 63.1629 Evaluate side-chains 158 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 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 1543 GLN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 176 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 123 optimal weight: 0.0770 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1202 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.166112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.139737 restraints weight = 42919.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.138890 restraints weight = 38958.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.140321 restraints weight = 31735.263| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15894 Z= 0.140 Angle : 0.637 12.964 21722 Z= 0.320 Chirality : 0.041 0.203 2459 Planarity : 0.004 0.060 2656 Dihedral : 11.691 95.244 2633 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 2.49 % Allowed : 18.16 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1783 helix: 1.00 (0.18), residues: 835 sheet: -0.81 (0.39), residues: 181 loop : -1.27 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1834 HIS 0.012 0.001 HIS K 368 PHE 0.027 0.002 PHE A1554 TYR 0.033 0.002 TYR A1148 ARG 0.004 0.000 ARG A2222 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 716) hydrogen bonds : angle 4.48564 ( 2059) covalent geometry : bond 0.00320 (15893) covalent geometry : angle 0.63713 (21722) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.839 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: 0.7104 (m) cc_final: 0.6812 (m) REVERT: A 63 ARG cc_start: 0.3173 (mmp-170) cc_final: 0.2352 (mmp80) REVERT: A 84 MET cc_start: 0.6059 (mpp) cc_final: 0.5563 (tpp) REVERT: A 338 LEU cc_start: 0.7378 (tp) cc_final: 0.7106 (pp) REVERT: A 1593 LEU cc_start: 0.0712 (OUTLIER) cc_final: -0.0302 (mt) REVERT: A 1664 PHE cc_start: 0.5015 (OUTLIER) cc_final: 0.4272 (m-10) REVERT: A 2151 MET cc_start: 0.6976 (mpp) cc_final: 0.6557 (mpp) REVERT: K 164 GLU cc_start: 0.3318 (OUTLIER) cc_final: 0.2886 (pp20) outliers start: 40 outliers final: 30 residues processed: 155 average time/residue: 0.2594 time to fit residues: 63.3573 Evaluate side-chains 151 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 15 PHE Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 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 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1989 LEU 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 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 462 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 181 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.166522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.139979 restraints weight = 43004.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.140159 restraints weight = 36813.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.141189 restraints weight = 29890.251| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15894 Z= 0.132 Angle : 0.633 11.129 21722 Z= 0.319 Chirality : 0.042 0.238 2459 Planarity : 0.005 0.084 2656 Dihedral : 11.679 96.113 2633 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.39 % Favored : 93.33 % Rotamer: Outliers : 2.18 % Allowed : 18.66 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1783 helix: 1.04 (0.18), residues: 835 sheet: -0.80 (0.40), residues: 181 loop : -1.26 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1834 HIS 0.013 0.001 HIS K 368 PHE 0.029 0.002 PHE A1554 TYR 0.027 0.002 TYR A1148 ARG 0.008 0.000 ARG A 602 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 716) hydrogen bonds : angle 4.45365 ( 2059) covalent geometry : bond 0.00298 (15893) covalent geometry : angle 0.63347 (21722) Misc. bond : bond 0.00017 ( 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 155 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7085 (m) cc_final: 0.6746 (m) REVERT: A 63 ARG cc_start: 0.3242 (mmp-170) cc_final: 0.2479 (mmp80) REVERT: A 863 TYR cc_start: 0.4614 (OUTLIER) cc_final: 0.4039 (t80) REVERT: A 1593 LEU cc_start: 0.0633 (OUTLIER) cc_final: -0.0371 (mt) REVERT: A 1664 PHE cc_start: 0.4797 (OUTLIER) cc_final: 0.4090 (m-10) REVERT: A 1929 TRP cc_start: 0.7493 (t60) cc_final: 0.6865 (t60) REVERT: A 2117 LEU cc_start: 0.4409 (OUTLIER) cc_final: 0.3485 (tp) REVERT: A 2151 MET cc_start: 0.6976 (mpp) cc_final: 0.6537 (mpp) REVERT: K 164 GLU cc_start: 0.3298 (OUTLIER) cc_final: 0.2864 (pp20) outliers start: 35 outliers final: 27 residues processed: 142 average time/residue: 0.3764 time to fit residues: 83.7431 Evaluate side-chains 142 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 3.425 ------------------------------------------------------------------------------- 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 15 PHE Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 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 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 174 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 150 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS A1147 GLN A1543 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.167447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.140741 restraints weight = 43127.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.140446 restraints weight = 35974.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.141682 restraints weight = 29992.120| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.3692 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= 0.119 Angle : 0.621 11.296 21722 Z= 0.311 Chirality : 0.041 0.208 2459 Planarity : 0.005 0.074 2656 Dihedral : 11.618 96.946 2633 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.66 % Favored : 94.05 % Rotamer: Outliers : 2.11 % Allowed : 18.84 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1783 helix: 1.10 (0.18), residues: 838 sheet: -0.75 (0.40), residues: 181 loop : -1.23 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1834 HIS 0.014 0.001 HIS K 368 PHE 0.028 0.001 PHE K 367 TYR 0.024 0.001 TYR A1148 ARG 0.005 0.000 ARG A2222 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 716) hydrogen bonds : angle 4.36654 ( 2059) covalent geometry : bond 0.00268 (15893) covalent geometry : angle 0.62094 (21722) Misc. bond : bond 0.00016 ( 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 153 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7027 (m) cc_final: 0.6747 (m) REVERT: A 63 ARG cc_start: 0.3142 (mmp-170) cc_final: 0.2875 (mmp80) REVERT: A 863 TYR cc_start: 0.4478 (OUTLIER) cc_final: 0.3984 (t80) REVERT: A 1593 LEU cc_start: 0.0524 (OUTLIER) cc_final: -0.0256 (mm) REVERT: A 1664 PHE cc_start: 0.4894 (OUTLIER) cc_final: 0.4128 (m-10) REVERT: A 2117 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.3540 (tp) REVERT: A 2151 MET cc_start: 0.6923 (mpp) cc_final: 0.6529 (mpp) REVERT: K 164 GLU cc_start: 0.3312 (OUTLIER) cc_final: 0.2850 (pp20) outliers start: 34 outliers final: 28 residues processed: 141 average time/residue: 0.2500 time to fit residues: 57.2451 Evaluate side-chains 148 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 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 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 1816 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 5 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS A1543 GLN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.167313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.140813 restraints weight = 43012.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.140500 restraints weight = 36449.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.141669 restraints weight = 29264.173| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 15894 Z= 0.177 Angle : 0.814 58.947 21722 Z= 0.449 Chirality : 0.048 1.206 2459 Planarity : 0.005 0.074 2656 Dihedral : 11.623 96.938 2633 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 1.99 % Allowed : 19.03 % Favored : 78.98 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1783 helix: 1.10 (0.18), residues: 838 sheet: -0.74 (0.40), residues: 181 loop : -1.22 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1834 HIS 0.015 0.001 HIS K 368 PHE 0.027 0.001 PHE K 367 TYR 0.022 0.001 TYR A1148 ARG 0.005 0.000 ARG K 170 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 716) hydrogen bonds : angle 4.37220 ( 2059) covalent geometry : bond 0.00380 (15893) covalent geometry : angle 0.81366 (21722) Misc. bond : bond 0.00000 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.39 seconds wall clock time: 107 minutes 22.68 seconds (6442.68 seconds total)