Starting phenix.real_space_refine on Fri Jul 3 20:22:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dga_27420/07_2026/8dga_27420.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 80 5.16 5 C 9663 2.51 5 N 2710 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15473 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1629, 13162 Classifications: {'peptide': 1629} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 1532} Chain breaks: 11 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 414 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 16} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1424 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.21 Number of scatterers: 15473 At special positions: 0 Unit cell: (158.53, 129.48, 145.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 42 15.00 O 2978 8.00 N 2710 7.00 C 9663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 589.6 milliseconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3460 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 12 sheets defined 48.6% alpha, 10.2% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 39 through 61 removed outlier: 4.137A pdb=" N ARG A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.612A pdb=" N TYR A 111 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 159 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 232 through 252 removed outlier: 4.141A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.088A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 4.199A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 344 removed outlier: 4.128A pdb=" N PHE A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.733A pdb=" N TYR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 374 Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 763 through 785 removed outlier: 3.538A pdb=" N CYS A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 4.030A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 835 removed outlier: 3.522A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 903 removed outlier: 3.725A pdb=" N ALA A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.750A pdb=" N GLU A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 940 Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 1000 through 1004 Processing helix chain 'A' and resid 1045 through 1062 Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1124 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.689A pdb=" N PHE A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 3.749A pdb=" N TYR A1180 " --> pdb=" O TYR A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1230 removed outlier: 4.083A pdb=" N LYS A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1229 " --> pdb=" O ARG A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1242 Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1538 through 1550 Processing helix chain 'A' and resid 1565 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1622 through 1629 Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1741 through 1764 Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.746A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1793 removed outlier: 3.514A pdb=" N LEU A1785 " --> pdb=" O ALA A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1798 removed outlier: 3.860A pdb=" N MET A1798 " --> pdb=" O GLY A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1825 removed outlier: 3.511A pdb=" N ALA A1823 " --> pdb=" O GLU A1819 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1825 " --> pdb=" O GLU A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1856 Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 Processing helix chain 'A' and resid 1993 through 2001 Processing helix chain 'A' and resid 2006 through 2014 removed outlier: 4.104A pdb=" N LEU A2010 " --> pdb=" O ASP A2006 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.955A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 removed outlier: 3.574A pdb=" N HIS A2079 " --> pdb=" O LEU A2075 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2105 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.754A pdb=" N GLY A2135 " --> pdb=" O PRO A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2174 removed outlier: 4.161A pdb=" N VAL A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix removed outlier: 4.439A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2187 removed outlier: 3.807A pdb=" N LEU A2183 " --> pdb=" O PRO A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2223 through 2239 removed outlier: 3.728A pdb=" N ALA A2227 " --> pdb=" O ASN A2223 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 188 through 205 removed outlier: 3.890A pdb=" N LEU K 204 " --> pdb=" O LEU K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 374 removed outlier: 3.740A pdb=" N PHE K 367 " --> pdb=" O LYS K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 393 through 405 Processing helix chain 'K' and resid 443 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.471A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 140 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 68 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU A 136 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU A 172 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 138 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU A 174 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 140 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 34 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 224 removed outlier: 5.732A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR A 222 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 496 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 497 " --> pdb=" O GLY A 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 877 through 878 removed outlier: 4.339A pdb=" N CYS A 850 " --> pdb=" O MET A1658 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 852 " --> pdb=" O ASN A1656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 952 through 956 Processing sheet with id=AA5, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 6.859A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 6.859A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A1087 " --> pdb=" O GLY A1007 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1153 through 1155 Processing sheet with id=AA8, first strand: chain 'A' and resid 1937 through 1941 removed outlier: 3.836A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2192 through 2193 removed outlier: 3.618A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2205 through 2206 Processing sheet with id=AB2, first strand: chain 'K' and resid 152 through 158 removed outlier: 3.805A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 409 through 412 685 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 1.68 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: 8682 17.90 - 35.80: 759 35.80 - 53.70: 120 53.70 - 71.59: 16 71.59 - 89.49: 9 Dihedral angle restraints: 9586 sinusoidal: 4261 harmonic: 5325 Sorted by residual: dihedral pdb=" CA VAL A 14 " pdb=" C VAL A 14 " pdb=" N PHE A 15 " pdb=" CA PHE A 15 " ideal model delta harmonic sigma weight residual -180.00 -119.71 -60.29 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LEU A2117 " pdb=" C LEU A2117 " pdb=" N SER A2118 " pdb=" CA SER A2118 " ideal model delta harmonic sigma weight residual 180.00 132.42 47.58 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" 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 9583 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: 0.010 Normalize map: mean=0, sd=1: 6.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 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 : 13.534 89.493 6126 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.01 % Favored : 92.65 % Rotamer: Outliers : 0.12 % Allowed : 0.81 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.18), residues: 1783 helix: -1.42 (0.15), residues: 818 sheet: -0.79 (0.39), residues: 160 loop : -1.77 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A2045 TYR 0.031 0.004 TYR A1175 PHE 0.047 0.004 PHE A 15 TRP 0.154 0.009 TRP A 108 HIS 0.014 0.002 HIS A1196 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.31 (15893) covalent geometry : angle 1.16602 / 0.60 (21722) hydrogen bonds : bond 0.14567 / 9.84 ( 716) hydrogen bonds : angle 6.89311 / 4.86 ( 2059) Misc. bond : bond 0.04738 / 2.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.467 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: 0.1245 time to fit residues: 34.0382 Evaluate side-chains 119 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS A 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS A 885 GLN A1189 GLN A1620 ASN A2016 HIS K 163 HIS K 405 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.169763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.143582 restraints weight = 42880.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.143028 restraints weight = 37221.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.144326 restraints weight = 31090.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.144399 restraints weight = 22284.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.144933 restraints weight = 19740.755| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.1489 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= 0.139 Angle : 0.670 14.762 21722 Z= 0.341 Chirality : 0.043 0.246 2459 Planarity : 0.005 0.061 2656 Dihedral : 8.121 97.051 2475 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.55 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 7.46 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1783 helix: -0.13 (0.17), residues: 830 sheet: -0.70 (0.40), residues: 167 loop : -1.50 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 775 TYR 0.022 0.002 TYR K 458 PHE 0.022 0.002 PHE A1552 TRP 0.046 0.003 TRP A 108 HIS 0.006 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15893) covalent geometry : angle 0.66995 / 0.34 (21722) hydrogen bonds : bond 0.04606 / 3.15 ( 716) hydrogen bonds : angle 5.00916 / 3.58 ( 2059) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.4032 (mpp) cc_final: 0.3496 (mmt) REVERT: A 2151 MET cc_start: 0.7065 (mpp) cc_final: 0.6775 (mpp) REVERT: A 2163 MET cc_start: 0.6973 (mpp) cc_final: 0.6661 (mmt) outliers start: 20 outliers final: 13 residues processed: 171 average time/residue: 0.1050 time to fit residues: 28.3585 Evaluate side-chains 140 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 8.9990 chunk 41 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS A 770 GLN A 787 ASN A1784 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.169681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.143357 restraints weight = 43298.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.143499 restraints weight = 34444.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.144616 restraints weight = 26085.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.144656 restraints weight = 18256.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.144943 restraints weight = 18129.367| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 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 0.034 15894 Z= 0.124 Angle : 0.614 11.946 21722 Z= 0.313 Chirality : 0.041 0.211 2459 Planarity : 0.005 0.069 2656 Dihedral : 7.689 98.582 2475 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.38 % Favored : 94.28 % Rotamer: Outliers : 1.62 % Allowed : 10.63 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1783 helix: 0.39 (0.17), residues: 837 sheet: -0.72 (0.40), residues: 172 loop : -1.38 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2204 TYR 0.017 0.001 TYR A1914 PHE 0.020 0.001 PHE K 367 TRP 0.023 0.002 TRP A 108 HIS 0.008 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15893) covalent geometry : angle 0.61440 / 0.31 (21722) hydrogen bonds : bond 0.04090 / 2.79 ( 716) hydrogen bonds : angle 4.65866 / 3.32 ( 2059) Misc. bond : bond 0.00002 / 0.00 ( 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 179 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.591 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: 0.6067 (mpp) cc_final: 0.5426 (tpp) REVERT: A 108 TRP cc_start: 0.4596 (m-10) cc_final: 0.4362 (m-10) REVERT: A 2151 MET cc_start: 0.6867 (mpp) cc_final: 0.6553 (mpp) REVERT: A 2163 MET cc_start: 0.7021 (mpp) cc_final: 0.6664 (mmt) REVERT: K 368 HIS cc_start: 0.1670 (m-70) cc_final: 0.1467 (m-70) outliers start: 26 outliers final: 19 residues processed: 169 average time/residue: 0.1061 time to fit residues: 27.8366 Evaluate side-chains 155 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 423 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 341 HIS ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 ASN ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1981 ASN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.161563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.135008 restraints weight = 43286.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.135855 restraints weight = 49172.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.137053 restraints weight = 36258.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.137891 restraints weight = 24575.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.138359 restraints weight = 22622.877| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 15894 Z= 0.277 Angle : 0.804 10.871 21722 Z= 0.412 Chirality : 0.047 0.225 2459 Planarity : 0.006 0.087 2656 Dihedral : 8.192 94.053 2475 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.23 % Favored : 92.43 % Rotamer: Outliers : 2.43 % Allowed : 13.68 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1783 helix: 0.03 (0.17), residues: 824 sheet: -0.74 (0.40), residues: 167 loop : -1.60 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1540 TYR 0.018 0.002 TYR A2115 PHE 0.022 0.003 PHE A1025 TRP 0.031 0.003 TRP A 848 HIS 0.017 0.002 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (15893) covalent geometry : angle 0.80371 / 0.41 (21722) hydrogen bonds : bond 0.05300 / 3.68 ( 716) hydrogen bonds : angle 5.30522 / 3.79 ( 2059) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5917 (mpp) cc_final: 0.5136 (tpp) REVERT: A 1112 MET cc_start: 0.6335 (tpt) cc_final: 0.6126 (tpt) REVERT: A 1202 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7075 (t0) REVERT: A 1544 GLN cc_start: 0.3599 (pt0) cc_final: 0.2534 (tm-30) REVERT: A 1664 PHE cc_start: 0.5277 (OUTLIER) cc_final: 0.4438 (m-10) REVERT: A 2151 MET cc_start: 0.7072 (mpp) cc_final: 0.6555 (mpp) REVERT: K 368 HIS cc_start: 0.2097 (m-70) cc_final: 0.1558 (m-70) outliers start: 39 outliers final: 28 residues processed: 168 average time/residue: 0.1021 time to fit residues: 26.6954 Evaluate side-chains 153 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 16 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 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 1903 ILE Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 105 optimal weight: 0.0070 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 HIS A 787 ASN A 885 GLN A1543 GLN A1736 ASN A1832 HIS A1833 HIS ** A1896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.166898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.141012 restraints weight = 43068.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.140694 restraints weight = 40801.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.142039 restraints weight = 34587.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.142378 restraints weight = 22495.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.142642 restraints weight = 21544.305| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15894 Z= 0.129 Angle : 0.624 8.117 21722 Z= 0.320 Chirality : 0.041 0.205 2459 Planarity : 0.005 0.063 2656 Dihedral : 7.562 96.635 2475 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 1.87 % Allowed : 16.29 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1783 helix: 0.56 (0.18), residues: 828 sheet: -0.69 (0.40), residues: 172 loop : -1.39 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2222 TYR 0.023 0.002 TYR A1148 PHE 0.018 0.001 PHE K 367 TRP 0.020 0.002 TRP A 108 HIS 0.007 0.001 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15893) covalent geometry : angle 0.62430 / 0.32 (21722) hydrogen bonds : bond 0.04029 / 2.79 ( 716) hydrogen bonds : angle 4.72517 / 3.38 ( 2059) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.410 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: 0.7066 (m) cc_final: 0.6833 (m) REVERT: A 108 TRP cc_start: 0.4609 (m-90) cc_final: 0.4251 (m-10) REVERT: A 1112 MET cc_start: 0.6505 (tpt) cc_final: 0.6285 (tpt) REVERT: A 1664 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.4430 (m-10) REVERT: A 1929 TRP cc_start: 0.7529 (t60) cc_final: 0.6984 (t60) REVERT: A 2151 MET cc_start: 0.6992 (mpp) cc_final: 0.6727 (mpp) REVERT: K 164 GLU cc_start: 0.3513 (OUTLIER) cc_final: 0.3115 (pp20) REVERT: K 368 HIS cc_start: 0.1695 (m-70) cc_final: 0.1445 (m-70) outliers start: 30 outliers final: 23 residues processed: 157 average time/residue: 0.0974 time to fit residues: 23.9168 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 : 0.565 ------------------------------------------------------------------------------- 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 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 HIS A 787 ASN A1543 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.166306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.140025 restraints weight = 43094.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.140189 restraints weight = 38776.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.141394 restraints weight = 31429.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.141671 restraints weight = 21828.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.141964 restraints weight = 21582.418| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15894 Z= 0.137 Angle : 0.616 9.250 21722 Z= 0.315 Chirality : 0.041 0.205 2459 Planarity : 0.004 0.061 2656 Dihedral : 7.324 89.941 2475 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.28 % Favored : 93.38 % Rotamer: Outliers : 2.55 % Allowed : 17.23 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1783 helix: 0.73 (0.18), residues: 831 sheet: -0.81 (0.39), residues: 179 loop : -1.40 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2098 TYR 0.022 0.002 TYR A 977 PHE 0.019 0.002 PHE K 180 TRP 0.019 0.002 TRP A1834 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15893) covalent geometry : angle 0.61639 / 0.31 (21722) hydrogen bonds : bond 0.03961 / 2.74 ( 716) hydrogen bonds : angle 4.61835 / 3.29 ( 2059) Misc. bond : bond 0.00006 / 0.00 ( 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 180 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.477 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: 0.6052 (mpp) cc_final: 0.5823 (mpp) REVERT: A 1112 MET cc_start: 0.6562 (tpt) cc_final: 0.6300 (tpt) REVERT: A 1593 LEU cc_start: 0.0899 (OUTLIER) cc_final: -0.0097 (mt) REVERT: A 1664 PHE cc_start: 0.5141 (OUTLIER) cc_final: 0.4389 (m-10) REVERT: A 1929 TRP cc_start: 0.7530 (t60) cc_final: 0.6924 (t60) REVERT: A 2117 LEU cc_start: 0.4654 (OUTLIER) cc_final: 0.3715 (tp) REVERT: A 2151 MET cc_start: 0.6937 (mpp) cc_final: 0.6514 (mpp) REVERT: K 164 GLU cc_start: 0.3392 (OUTLIER) cc_final: 0.2999 (pp20) outliers start: 41 outliers final: 25 residues processed: 167 average time/residue: 0.1044 time to fit residues: 27.6224 Evaluate side-chains 156 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1903 ILE 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 366 GLN Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 78 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1202 ASN A1543 GLN ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 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 = 0.4854 r_free = 0.4854 target = 0.165237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.139527 restraints weight = 42910.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.138821 restraints weight = 45581.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.140198 restraints weight = 38219.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.140965 restraints weight = 25578.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.141209 restraints weight = 24336.598| |-----------------------------------------------------------------------------| r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15894 Z= 0.166 Angle : 0.662 14.139 21722 Z= 0.335 Chirality : 0.042 0.204 2459 Planarity : 0.004 0.061 2656 Dihedral : 7.387 87.257 2475 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.62 % Favored : 93.10 % Rotamer: Outliers : 2.74 % Allowed : 17.85 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1783 helix: 0.69 (0.17), residues: 831 sheet: -0.73 (0.40), residues: 174 loop : -1.42 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2222 TYR 0.034 0.002 TYR A1148 PHE 0.018 0.002 PHE A1552 TRP 0.018 0.002 TRP A1834 HIS 0.014 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15893) covalent geometry : angle 0.66234 / 0.33 (21722) hydrogen bonds : bond 0.04178 / 2.90 ( 716) hydrogen bonds : angle 4.71030 / 3.36 ( 2059) Misc. bond : bond 0.00010 / 0.01 ( 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 175 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.3120 (mmp-170) cc_final: 0.2375 (mmp80) REVERT: A 100 MET cc_start: 0.6500 (tpp) cc_final: 0.6205 (tmm) REVERT: A 1112 MET cc_start: 0.6606 (tpt) cc_final: 0.6360 (tpt) REVERT: A 1593 LEU cc_start: 0.0798 (OUTLIER) cc_final: -0.0165 (mt) REVERT: A 1664 PHE cc_start: 0.5008 (OUTLIER) cc_final: 0.4282 (m-10) REVERT: A 1929 TRP cc_start: 0.7546 (t60) cc_final: 0.7005 (t60) REVERT: A 2117 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.3702 (tp) REVERT: A 2151 MET cc_start: 0.7025 (mpp) cc_final: 0.6610 (mpp) REVERT: K 164 GLU cc_start: 0.3320 (OUTLIER) cc_final: 0.2897 (pp20) outliers start: 44 outliers final: 32 residues processed: 158 average time/residue: 0.1140 time to fit residues: 28.3257 Evaluate side-chains 160 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 204 GLU 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 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1153 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 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 2129 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A1080 ASN A1543 GLN A1896 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.167681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.141876 restraints weight = 43154.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.140856 restraints weight = 39942.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.142584 restraints weight = 32019.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.142905 restraints weight = 21488.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.143240 restraints weight = 21500.899| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.3431 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= 0.118 Angle : 0.625 13.202 21722 Z= 0.315 Chirality : 0.041 0.210 2459 Planarity : 0.004 0.072 2656 Dihedral : 7.190 90.820 2475 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.66 % Favored : 94.05 % Rotamer: Outliers : 2.43 % Allowed : 18.47 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1783 helix: 0.96 (0.18), residues: 831 sheet: -0.58 (0.40), residues: 171 loop : -1.29 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.031 0.001 TYR A1148 PHE 0.028 0.001 PHE K 367 TRP 0.019 0.002 TRP A1834 HIS 0.012 0.001 HIS K 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15893) covalent geometry : angle 0.62541 / 0.31 (21722) hydrogen bonds : bond 0.03724 / 2.58 ( 716) hydrogen bonds : angle 4.49283 / 3.21 ( 2059) Misc. bond : bond 0.00001 / 0.00 ( 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 168 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.606 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: 0.7016 (m) cc_final: 0.6760 (m) REVERT: A 63 ARG cc_start: 0.3086 (mmp-170) cc_final: 0.2448 (mmp80) REVERT: A 84 MET cc_start: 0.6067 (mpp) cc_final: 0.5609 (tpp) REVERT: A 178 LEU cc_start: 0.6806 (mt) cc_final: 0.6408 (mp) REVERT: A 1593 LEU cc_start: 0.0735 (OUTLIER) cc_final: -0.0038 (mm) REVERT: A 1664 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4251 (m-10) REVERT: A 1929 TRP cc_start: 0.7464 (t60) cc_final: 0.6872 (t60) REVERT: A 2151 MET cc_start: 0.6882 (mpp) cc_final: 0.6515 (mpp) REVERT: K 164 GLU cc_start: 0.3296 (OUTLIER) cc_final: 0.2875 (pp20) outliers start: 39 outliers final: 27 residues processed: 156 average time/residue: 0.1149 time to fit residues: 28.6509 Evaluate side-chains 149 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1677 GLU Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 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 366 GLN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4234 > 50: distance: 1 - 16: 28.723 distance: 12 - 16: 28.075 distance: 16 - 17: 32.725 distance: 17 - 18: 41.706 distance: 17 - 20: 30.601 distance: 18 - 19: 4.753 distance: 20 - 21: 12.130 distance: 23 - 24: 44.652 distance: 24 - 25: 36.372 distance: 24 - 27: 21.949 distance: 27 - 28: 17.873 distance: 28 - 29: 14.957 distance: 28 - 31: 13.144 distance: 29 - 30: 41.283 distance: 29 - 33: 19.274 distance: 31 - 32: 15.718 distance: 33 - 34: 4.455 distance: 34 - 35: 26.032 distance: 34 - 37: 6.156 distance: 35 - 36: 19.620 distance: 35 - 41: 24.629 distance: 37 - 38: 4.781 distance: 38 - 39: 24.730 distance: 38 - 40: 26.257 distance: 41 - 42: 29.090 distance: 42 - 43: 17.545 distance: 42 - 45: 13.116 distance: 43 - 44: 24.910 distance: 43 - 46: 46.828 distance: 46 - 47: 5.228 distance: 47 - 48: 35.391 distance: 47 - 50: 17.338 distance: 48 - 49: 3.318 distance: 48 - 51: 53.305 distance: 51 - 52: 31.520 distance: 52 - 53: 55.027 distance: 52 - 55: 39.344 distance: 53 - 54: 56.402 distance: 53 - 63: 27.320 distance: 56 - 57: 3.531 distance: 56 - 58: 20.811 distance: 57 - 59: 30.467 distance: 58 - 60: 36.553 distance: 59 - 61: 39.833 distance: 60 - 61: 11.739 distance: 63 - 64: 23.548 distance: 64 - 65: 41.120 distance: 64 - 67: 40.517 distance: 65 - 66: 18.989 distance: 65 - 74: 47.049 distance: 67 - 68: 35.709 distance: 68 - 69: 49.290 distance: 69 - 70: 22.408 distance: 71 - 72: 59.548 distance: 71 - 73: 46.378 distance: 74 - 75: 20.099 distance: 74 - 80: 25.587 distance: 75 - 76: 7.609 distance: 75 - 78: 11.721 distance: 76 - 77: 39.789 distance: 76 - 81: 23.788 distance: 78 - 79: 42.390 distance: 79 - 80: 24.454 distance: 81 - 82: 14.953 distance: 82 - 83: 21.693 distance: 82 - 85: 37.425 distance: 83 - 84: 14.876 distance: 83 - 90: 27.730 distance: 85 - 86: 11.408 distance: 86 - 87: 48.578 distance: 87 - 88: 6.155 distance: 88 - 89: 39.495