Starting phenix.real_space_refine on Tue Dec 31 15:28:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dga_27420/12_2024/8dga_27420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dga_27420/12_2024/8dga_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_27420/12_2024/8dga_27420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dga_27420/12_2024/8dga_27420.map" model { file = "/net/cci-nas-00/data/ceres_data/8dga_27420/12_2024/8dga_27420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dga_27420/12_2024/8dga_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 9.92, per 1000 atoms: 0.64 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: 4.25 Conformation dependent library (CDL) restraints added in 2.0 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: 5.78 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: 7.27 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3969 1.33 - 1.46: 3438 1.46 - 1.58: 8294 1.58 - 1.70: 83 1.70 - 1.82: 109 Bond restraints: 15893 Sorted by residual: bond pdb=" C GLU A 931 " pdb=" N PRO A 932 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.38e-02 5.25e+03 6.95e+00 bond pdb=" CG LEU A1915 " pdb=" CD1 LEU A1915 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.70e+00 bond pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " ideal model delta sigma weight residual 1.520 1.591 -0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" CG LEU A2147 " pdb=" CD1 LEU A2147 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.52e+00 bond pdb=" C LEU A 867 " pdb=" N PRO A 868 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.25e-02 6.40e+03 5.20e+00 ... (remaining 15888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 21234 3.37 - 6.75: 414 6.75 - 10.12: 59 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: 8738 17.90 - 35.80: 782 35.80 - 53.70: 147 53.70 - 71.59: 60 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: 2256 0.105 - 0.211: 184 0.211 - 0.316: 14 0.316 - 0.421: 3 0.421 - 0.527: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CG LEU A 496 " pdb=" CB LEU A 496 " pdb=" CD1 LEU A 496 " pdb=" CD2 LEU A 496 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CB ILE A1829 " pdb=" CA ILE A1829 " pdb=" CG1 ILE A1829 " pdb=" CG2 ILE A1829 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE A1010 " pdb=" CA ILE A1010 " pdb=" CG1 ILE A1010 " pdb=" CG2 ILE A1010 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2456 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 108 " 0.058 2.00e-02 2.50e+03 6.16e-02 9.49e+01 pdb=" CG TRP A 108 " -0.154 2.00e-02 2.50e+03 pdb=" CD1 TRP A 108 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TRP A 108 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 108 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 108 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 108 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 108 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 108 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 848 " -0.032 2.00e-02 2.50e+03 4.46e-02 4.97e+01 pdb=" CG TRP A 848 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 848 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP A 848 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 848 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 848 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 848 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 848 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 848 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 848 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A2053 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN A2053 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN A2053 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A2054 " 0.021 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1725 2.75 - 3.29: 15109 3.29 - 3.82: 27254 3.82 - 4.36: 31780 4.36 - 4.90: 51164 Nonbonded interactions: 127032 Sorted by model distance: nonbonded pdb=" O ARG A1207 " pdb=" O2' A F 50 " model vdw 2.210 3.040 nonbonded pdb=" O LEU K 459 " pdb=" OG1 THR K 463 " model vdw 2.264 3.040 nonbonded pdb=" O PHE A 841 " pdb=" OG SER A2089 " model vdw 2.266 3.040 nonbonded pdb=" O VAL A1767 " pdb=" NH1 ARG A2030 " model vdw 2.283 3.120 nonbonded pdb=" O GLY A 294 " pdb=" OG1 THR A 298 " model vdw 2.283 3.040 ... (remaining 127027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.650 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.040 Find NCS groups from input model: 0.140 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- 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 0.093 15893 Z= 0.455 Angle : 1.166 16.872 21722 Z= 0.598 Chirality : 0.062 0.527 2459 Planarity : 0.009 0.121 2656 Dihedral : 14.987 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 *********************** 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 : 1.555 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: 0.3015 time to fit residues: 81.8947 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 : 1.797 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15893 Z= 0.185 Angle : 0.661 14.646 21722 Z= 0.336 Chirality : 0.042 0.241 2459 Planarity : 0.005 0.060 2656 Dihedral : 12.825 97.072 2633 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 1.18 % Allowed : 7.77 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: -1.16 (0.19), residues: 1783 helix: -0.08 (0.17), residues: 830 sheet: -0.69 (0.40), residues: 167 loop : -1.48 (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 0.001 TYR K 458 ARG 0.009 0.001 ARG A 775 *********************** 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 184 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.3915 (mpp) cc_final: 0.3457 (mmt) REVERT: A 1609 MET cc_start: 0.5211 (tpp) cc_final: 0.4951 (tpp) REVERT: A 2151 MET cc_start: 0.6936 (mpp) cc_final: 0.6634 (mpp) REVERT: A 2163 MET cc_start: 0.7413 (mpp) cc_final: 0.6960 (mmt) REVERT: K 405 ASN cc_start: 0.6320 (t0) cc_final: 0.6061 (t0) outliers start: 19 outliers final: 13 residues processed: 175 average time/residue: 0.2838 time to fit residues: 76.3551 Evaluate side-chains 139 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 101 GLN A 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 787 ASN A1784 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15893 Z= 0.200 Angle : 0.631 12.219 21722 Z= 0.321 Chirality : 0.041 0.208 2459 Planarity : 0.005 0.064 2656 Dihedral : 12.529 96.822 2633 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.83 % Favored : 93.83 % Rotamer: Outliers : 1.87 % Allowed : 10.76 % Favored : 87.38 % 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: -0.78 (0.20), residues: 1783 helix: 0.35 (0.17), residues: 835 sheet: -0.74 (0.40), residues: 172 loop : -1.38 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1834 HIS 0.015 0.001 HIS K 194 PHE 0.020 0.001 PHE K 367 TYR 0.016 0.001 TYR A1148 ARG 0.006 0.000 ARG A2204 *********************** 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: 30 poor density : 149 time to evaluate : 1.609 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: 0.5877 (mpp) cc_final: 0.5351 (tpp) REVERT: A 108 TRP cc_start: 0.5338 (m-10) cc_final: 0.5125 (m-10) REVERT: A 1609 MET cc_start: 0.4844 (tpp) cc_final: 0.4296 (tpp) REVERT: A 1613 LYS cc_start: 0.8293 (mmtp) cc_final: 0.8064 (mmtp) REVERT: A 2151 MET cc_start: 0.6861 (mpp) cc_final: 0.6500 (mpp) REVERT: A 2163 MET cc_start: 0.7497 (mpp) cc_final: 0.6982 (mmt) REVERT: K 368 HIS cc_start: 0.1589 (m-70) cc_final: 0.1313 (m-70) REVERT: K 405 ASN cc_start: 0.6176 (t0) cc_final: 0.5897 (t0) outliers start: 30 outliers final: 20 residues processed: 166 average time/residue: 0.2694 time to fit residues: 69.7286 Evaluate side-chains 153 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 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 164 optimal weight: 9.9990 chunk 125 optimal weight: 0.0670 chunk 86 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 176 optimal weight: 0.0980 chunk 87 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 A1896 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15893 Z= 0.156 Angle : 0.587 11.023 21722 Z= 0.299 Chirality : 0.040 0.203 2459 Planarity : 0.005 0.086 2656 Dihedral : 12.227 98.771 2633 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.27 % Favored : 94.39 % Rotamer: Outliers : 1.68 % Allowed : 12.81 % Favored : 85.51 % 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: -0.42 (0.20), residues: 1783 helix: 0.69 (0.18), residues: 837 sheet: -0.53 (0.40), residues: 172 loop : -1.27 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1834 HIS 0.006 0.001 HIS A 112 PHE 0.019 0.001 PHE K 367 TYR 0.014 0.001 TYR A 322 ARG 0.008 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.779 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: 0.7336 (m) cc_final: 0.7029 (m) REVERT: A 84 MET cc_start: 0.5886 (mpp) cc_final: 0.5352 (tpp) REVERT: A 1112 MET cc_start: 0.6365 (tpt) cc_final: 0.6094 (tpt) REVERT: A 1609 MET cc_start: 0.4834 (tpp) cc_final: 0.4226 (tpp) REVERT: A 2151 MET cc_start: 0.6785 (mpp) cc_final: 0.6486 (mpp) REVERT: A 2163 MET cc_start: 0.7452 (mpp) cc_final: 0.7033 (mmt) REVERT: K 368 HIS cc_start: 0.1599 (m-70) cc_final: 0.1394 (m-70) REVERT: K 405 ASN cc_start: 0.6085 (t0) cc_final: 0.5809 (t0) outliers start: 27 outliers final: 21 residues processed: 166 average time/residue: 0.2671 time to fit residues: 69.4279 Evaluate side-chains 153 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 341 HIS A 787 ASN A1543 GLN A2223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15893 Z= 0.194 Angle : 0.601 8.502 21722 Z= 0.306 Chirality : 0.041 0.199 2459 Planarity : 0.004 0.056 2656 Dihedral : 12.068 96.373 2633 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.78 % Favored : 93.89 % Rotamer: Outliers : 2.24 % Allowed : 13.74 % Favored : 84.02 % 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: -0.28 (0.20), residues: 1783 helix: 0.86 (0.18), residues: 831 sheet: -0.40 (0.41), residues: 172 loop : -1.28 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1834 HIS 0.005 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.024 0.001 TYR A1148 ARG 0.004 0.000 ARG A2098 *********************** 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 181 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7426 (m) cc_final: 0.7113 (m) REVERT: A 1112 MET cc_start: 0.6376 (tpt) cc_final: 0.6116 (tpt) REVERT: A 1609 MET cc_start: 0.5372 (tpp) cc_final: 0.4835 (tpp) REVERT: A 1664 PHE cc_start: 0.4735 (OUTLIER) cc_final: 0.3884 (m-10) REVERT: A 1892 LEU cc_start: 0.7582 (tp) cc_final: 0.7255 (tp) REVERT: A 2151 MET cc_start: 0.6811 (mpp) cc_final: 0.6449 (mpp) REVERT: K 164 GLU cc_start: 0.3601 (OUTLIER) cc_final: 0.3279 (pp20) REVERT: K 368 HIS cc_start: 0.1733 (m-70) cc_final: 0.1483 (m-70) REVERT: K 405 ASN cc_start: 0.5877 (t0) cc_final: 0.5621 (t0) outliers start: 36 outliers final: 25 residues processed: 166 average time/residue: 0.2765 time to fit residues: 71.6139 Evaluate side-chains 157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1621 GLU Chi-restraints excluded: chain A residue 1664 PHE 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 A residue 2130 VAL 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 59 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 787 ASN A1620 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15893 Z= 0.206 Angle : 0.615 14.053 21722 Z= 0.310 Chirality : 0.041 0.199 2459 Planarity : 0.004 0.055 2656 Dihedral : 12.018 95.355 2633 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.78 % Favored : 93.89 % Rotamer: Outliers : 2.30 % Allowed : 15.17 % Favored : 82.52 % 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: 0.91 (0.18), residues: 834 sheet: -0.33 (0.41), residues: 167 loop : -1.31 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1834 HIS 0.005 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.029 0.001 TYR A1148 ARG 0.004 0.000 ARG A1540 *********************** 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: 37 poor density : 136 time to evaluate : 1.860 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: 0.7474 (m) cc_final: 0.7167 (m) REVERT: A 900 LEU cc_start: 0.6131 (mt) cc_final: 0.5928 (mt) REVERT: A 1112 MET cc_start: 0.6411 (tpt) cc_final: 0.6161 (tpt) REVERT: A 1593 LEU cc_start: 0.1271 (OUTLIER) cc_final: 0.0125 (mt) REVERT: A 1664 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4012 (m-10) REVERT: A 2151 MET cc_start: 0.6832 (mpp) cc_final: 0.6489 (mpp) REVERT: K 164 GLU cc_start: 0.3661 (OUTLIER) cc_final: 0.3298 (pp20) REVERT: K 405 ASN cc_start: 0.5950 (t0) cc_final: 0.5669 (m-40) outliers start: 37 outliers final: 26 residues processed: 158 average time/residue: 0.2749 time to fit residues: 68.4112 Evaluate side-chains 155 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1544 GLN Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 129 optimal weight: 0.3980 chunk 149 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 787 ASN A1080 ASN ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15893 Z= 0.183 Angle : 0.603 11.720 21722 Z= 0.304 Chirality : 0.041 0.201 2459 Planarity : 0.004 0.055 2656 Dihedral : 11.988 95.649 2633 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.89 % Favored : 93.83 % Rotamer: Outliers : 2.36 % Allowed : 15.86 % Favored : 81.78 % 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: -0.20 (0.20), residues: 1783 helix: 1.07 (0.18), residues: 830 sheet: -0.77 (0.39), residues: 184 loop : -1.31 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1834 HIS 0.012 0.001 HIS K 368 PHE 0.018 0.001 PHE K 180 TYR 0.032 0.001 TYR A1148 ARG 0.003 0.000 ARG A2222 *********************** 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 172 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.576 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: 0.7440 (m) cc_final: 0.7115 (m) REVERT: A 338 LEU cc_start: 0.7733 (tp) cc_final: 0.7229 (pp) REVERT: A 900 LEU cc_start: 0.6143 (mt) cc_final: 0.5918 (mt) REVERT: A 1112 MET cc_start: 0.6417 (tpt) cc_final: 0.6191 (tpt) REVERT: A 1593 LEU cc_start: 0.1184 (OUTLIER) cc_final: 0.0022 (mt) REVERT: A 1664 PHE cc_start: 0.4919 (OUTLIER) cc_final: 0.4096 (m-10) REVERT: A 2117 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.3423 (tp) REVERT: A 2151 MET cc_start: 0.6841 (mpp) cc_final: 0.6463 (mpp) REVERT: K 164 GLU cc_start: 0.3635 (OUTLIER) cc_final: 0.3250 (pp20) REVERT: K 405 ASN cc_start: 0.6003 (t0) cc_final: 0.5739 (m-40) outliers start: 38 outliers final: 24 residues processed: 158 average time/residue: 0.2668 time to fit residues: 65.8091 Evaluate side-chains 154 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 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 2158 HIS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15893 Z= 0.199 Angle : 0.617 12.061 21722 Z= 0.310 Chirality : 0.041 0.203 2459 Planarity : 0.004 0.055 2656 Dihedral : 11.970 94.946 2633 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.17 % Favored : 93.55 % Rotamer: Outliers : 2.43 % Allowed : 16.36 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.20), residues: 1783 helix: 1.12 (0.18), residues: 829 sheet: -0.75 (0.39), residues: 182 loop : -1.30 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1834 HIS 0.011 0.001 HIS K 368 PHE 0.019 0.001 PHE K 367 TYR 0.034 0.001 TYR A1148 ARG 0.004 0.000 ARG A2222 *********************** 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 173 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.679 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: 0.7501 (m) cc_final: 0.7171 (m) REVERT: A 338 LEU cc_start: 0.7591 (tp) cc_final: 0.7150 (pp) REVERT: A 900 LEU cc_start: 0.6174 (mt) cc_final: 0.5953 (mt) REVERT: A 1593 LEU cc_start: 0.0720 (OUTLIER) cc_final: -0.0440 (mt) REVERT: A 1664 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.4188 (m-10) REVERT: A 2014 MET cc_start: 0.6731 (mmm) cc_final: 0.6482 (mmm) REVERT: A 2151 MET cc_start: 0.6886 (mpp) cc_final: 0.6530 (mpp) REVERT: K 164 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.3230 (pp20) REVERT: K 405 ASN cc_start: 0.5886 (t0) cc_final: 0.5626 (m-40) outliers start: 39 outliers final: 28 residues processed: 161 average time/residue: 0.2619 time to fit residues: 66.9666 Evaluate side-chains 156 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 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 1903 ILE Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.0020 chunk 148 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 341 HIS A1147 GLN A1833 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15893 Z= 0.178 Angle : 0.610 11.671 21722 Z= 0.306 Chirality : 0.041 0.205 2459 Planarity : 0.004 0.058 2656 Dihedral : 11.943 95.984 2633 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.72 % Favored : 94.00 % Rotamer: Outliers : 2.24 % Allowed : 16.98 % Favored : 80.78 % 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: -0.06 (0.20), residues: 1783 helix: 1.21 (0.18), residues: 832 sheet: -0.69 (0.39), residues: 182 loop : -1.27 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1834 HIS 0.015 0.001 HIS K 368 PHE 0.026 0.001 PHE K 367 TYR 0.033 0.001 TYR A1148 ARG 0.005 0.000 ARG A2222 *********************** 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 171 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7466 (m) cc_final: 0.7124 (m) REVERT: A 338 LEU cc_start: 0.7459 (tp) cc_final: 0.7065 (pp) REVERT: A 900 LEU cc_start: 0.6184 (mt) cc_final: 0.5957 (mt) REVERT: A 1593 LEU cc_start: 0.0965 (OUTLIER) cc_final: -0.0172 (mt) REVERT: A 1664 PHE cc_start: 0.4860 (OUTLIER) cc_final: 0.4110 (m-10) REVERT: A 2117 LEU cc_start: 0.4193 (OUTLIER) cc_final: 0.3250 (tp) REVERT: A 2151 MET cc_start: 0.6795 (mpp) cc_final: 0.6411 (mpp) REVERT: K 164 GLU cc_start: 0.3551 (OUTLIER) cc_final: 0.3170 (pp20) REVERT: K 405 ASN cc_start: 0.5865 (t0) cc_final: 0.5603 (m-40) outliers start: 36 outliers final: 26 residues processed: 156 average time/residue: 0.2711 time to fit residues: 67.7906 Evaluate side-chains 157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.6202 ------------------------------------------------------------------------------- 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15893 Z= 0.169 Angle : 0.623 14.408 21722 Z= 0.309 Chirality : 0.041 0.208 2459 Planarity : 0.004 0.058 2656 Dihedral : 11.906 96.343 2633 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.55 % Favored : 94.17 % Rotamer: Outliers : 1.93 % Allowed : 17.48 % Favored : 80.60 % 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: 0.06 (0.21), residues: 1783 helix: 1.29 (0.18), residues: 833 sheet: -0.63 (0.40), residues: 182 loop : -1.19 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1834 HIS 0.014 0.001 HIS K 368 PHE 0.028 0.001 PHE K 367 TYR 0.030 0.001 TYR A1148 ARG 0.005 0.000 ARG A2222 ********************** 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 166 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.573 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: 0.7385 (m) cc_final: 0.7063 (m) REVERT: A 63 ARG cc_start: 0.3468 (mmp-170) cc_final: 0.2580 (mmp80) REVERT: A 338 LEU cc_start: 0.7415 (tp) cc_final: 0.7007 (pp) REVERT: A 863 TYR cc_start: 0.4546 (OUTLIER) cc_final: 0.4058 (t80) REVERT: A 900 LEU cc_start: 0.6071 (mt) cc_final: 0.5831 (mt) REVERT: A 1593 LEU cc_start: 0.0651 (OUTLIER) cc_final: -0.0427 (mt) REVERT: A 1664 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.4183 (m-10) REVERT: A 2117 LEU cc_start: 0.4158 (OUTLIER) cc_final: 0.3178 (tp) REVERT: A 2151 MET cc_start: 0.6803 (mpp) cc_final: 0.6445 (mpp) REVERT: K 164 GLU cc_start: 0.3427 (OUTLIER) cc_final: 0.3048 (pp20) REVERT: K 405 ASN cc_start: 0.5897 (t0) cc_final: 0.5630 (m-40) outliers start: 31 outliers final: 24 residues processed: 154 average time/residue: 0.2666 time to fit residues: 65.4965 Evaluate side-chains 157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 588 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 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 1932 VAL Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 145 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 GLN 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 = 0.167563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.140764 restraints weight = 42933.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.140192 restraints weight = 33868.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.141360 restraints weight = 29635.188| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15893 Z= 0.190 Angle : 0.631 13.594 21722 Z= 0.315 Chirality : 0.041 0.206 2459 Planarity : 0.004 0.058 2656 Dihedral : 11.904 95.471 2633 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 2.18 % Allowed : 17.54 % Favored : 80.29 % 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: 0.02 (0.21), residues: 1783 helix: 1.26 (0.18), residues: 833 sheet: -0.64 (0.40), residues: 182 loop : -1.21 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1834 HIS 0.015 0.001 HIS K 368 PHE 0.029 0.002 PHE A 15 TYR 0.034 0.001 TYR A1148 ARG 0.005 0.000 ARG A2222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3191.29 seconds wall clock time: 60 minutes 39.37 seconds (3639.37 seconds total)