Starting phenix.real_space_refine on Fri Feb 16 19:09:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg5_27416/02_2024/8dg5_27416_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg5_27416/02_2024/8dg5_27416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg5_27416/02_2024/8dg5_27416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg5_27416/02_2024/8dg5_27416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg5_27416/02_2024/8dg5_27416_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg5_27416/02_2024/8dg5_27416_updated.pdb" } resolution = 3.26 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= 0.039 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: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 11 5.21 5 S 88 5.16 5 C 10124 2.51 5 N 2859 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 552": "OE1" <-> "OE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2026": "OD1" <-> "OD2" Residue "A ASP 2097": "OD1" <-> "OD2" Residue "A GLU 2187": "OE1" <-> "OE2" Residue "A GLU 2189": "OE1" <-> "OE2" Residue "A PHE 2212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16269 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 13175 Classifications: {'peptide': 1635} Link IDs: {'PTRANS': 98, 'TRANS': 1536} Chain breaks: 14 Chain: "E" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1057 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 23, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 48} Chain breaks: 1 Chain: "K" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2005 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' MG': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna2p': 1} Link IDs: {None: 8} Time building chain proxies: 9.46, per 1000 atoms: 0.58 Number of scatterers: 16269 At special positions: 0 Unit cell: (156.04, 128.65, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 51 15.00 Mg 11 11.99 O 3136 8.00 N 2859 7.00 C 10124 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 - 3.50 Amino acid : False - 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: 7.37 Conformation dependent library (CDL) restraints added in 2.9 seconds 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 11 sheets defined 41.7% alpha, 7.2% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 8.48 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 40 through 58 Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.575A pdb=" N MET A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 146 through 156 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.763A pdb=" N SER A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.340A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 345 removed outlier: 3.656A pdb=" N ARG A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 504 through 518 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.675A pdb=" N ARG A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.802A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.016A pdb=" N ILE A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.516A pdb=" N ASN A1057 " --> pdb=" O ASN A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1107 Processing helix chain 'A' and resid 1118 through 1123 Processing helix chain 'A' and resid 1172 through 1179 Processing helix chain 'A' and resid 1221 through 1228 Processing helix chain 'A' and resid 1249 through 1281 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1526 through 1534 Processing helix chain 'A' and resid 1536 through 1548 removed outlier: 3.740A pdb=" N ARG A1540 " --> pdb=" O ASN A1536 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A1546 " --> pdb=" O TYR A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1580 Processing helix chain 'A' and resid 1608 through 1615 Processing helix chain 'A' and resid 1624 through 1628 Processing helix chain 'A' and resid 1636 through 1649 Processing helix chain 'A' and resid 1723 through 1730 Processing helix chain 'A' and resid 1733 through 1735 No H-bonds generated for 'chain 'A' and resid 1733 through 1735' Processing helix chain 'A' and resid 1742 through 1763 removed outlier: 3.780A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1769 through 1779 removed outlier: 4.087A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1791 Processing helix chain 'A' and resid 1795 through 1797 No H-bonds generated for 'chain 'A' and resid 1795 through 1797' Processing helix chain 'A' and resid 1820 through 1823 No H-bonds generated for 'chain 'A' and resid 1820 through 1823' Processing helix chain 'A' and resid 1836 through 1845 Processing helix chain 'A' and resid 1848 through 1853 Processing helix chain 'A' and resid 1900 through 1930 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1982 through 1989 Processing helix chain 'A' and resid 1994 through 2000 Processing helix chain 'A' and resid 2007 through 2014 Processing helix chain 'A' and resid 2029 through 2048 removed outlier: 3.715A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2064 removed outlier: 3.923A pdb=" N ARG A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2078 Processing helix chain 'A' and resid 2090 through 2105 Processing helix chain 'A' and resid 2132 through 2149 removed outlier: 3.829A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2173 removed outlier: 4.147A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2179 through 2186 Processing helix chain 'A' and resid 2224 through 2239 Processing helix chain 'K' and resid 136 through 144 Processing helix chain 'K' and resid 189 through 204 Processing helix chain 'K' and resid 253 through 261 Processing helix chain 'K' and resid 301 through 318 Processing helix chain 'K' and resid 359 through 373 Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 394 through 404 Processing helix chain 'K' and resid 444 through 463 Processing sheet with id= A, first strand: chain 'A' and resid 220 through 225 removed outlier: 4.103A pdb=" N HIS A 610 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 852 through 855 Processing sheet with id= C, first strand: chain 'A' and resid 952 through 956 Processing sheet with id= D, first strand: chain 'A' and resid 1095 through 1097 removed outlier: 10.646A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1071 through 1073 removed outlier: 3.974A pdb=" N LEU A1072 " --> pdb=" O TYR A1815 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.683A pdb=" N MET A1137 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1153 through 1155 Processing sheet with id= H, first strand: chain 'A' and resid 1936 through 1941 removed outlier: 3.717A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 181 through 186 removed outlier: 5.876A pdb=" N ARG K 170 " --> pdb=" O LEU K 155 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU K 155 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER K 172 " --> pdb=" O TYR K 153 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR K 153 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 293 through 298 removed outlier: 3.577A pdb=" N THR K 273 " --> pdb=" O THR K 284 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA K 286 " --> pdb=" O THR K 271 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR K 271 " --> pdb=" O ALA K 286 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER K 288 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR K 269 " --> pdb=" O SER K 288 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 409 through 413 568 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3529 1.33 - 1.57: 12958 1.57 - 1.80: 200 1.80 - 2.04: 27 2.04 - 2.28: 1 Bond restraints: 16715 Sorted by residual: bond pdb=" CB PRO A2188 " pdb=" CG PRO A2188 " ideal model delta sigma weight residual 1.492 2.280 -0.788 5.00e-02 4.00e+02 2.49e+02 bond pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 1.503 1.091 0.412 3.40e-02 8.65e+02 1.47e+02 bond pdb=" CG PRO K 251 " pdb=" CD PRO K 251 " ideal model delta sigma weight residual 1.503 1.094 0.409 3.40e-02 8.65e+02 1.45e+02 bond pdb=" CG PRO K 165 " pdb=" CD PRO K 165 " ideal model delta sigma weight residual 1.503 1.125 0.378 3.40e-02 8.65e+02 1.24e+02 bond pdb=" CB PRO K 251 " pdb=" CG PRO K 251 " ideal model delta sigma weight residual 1.492 1.206 0.286 5.00e-02 4.00e+02 3.27e+01 ... (remaining 16710 not shown) Histogram of bond angle deviations from ideal: 25.34 - 56.26: 1 56.26 - 87.18: 5 87.18 - 118.10: 12944 118.10 - 149.02: 9925 149.02 - 179.94: 2 Bond angle restraints: 22877 Sorted by residual: angle pdb=" CB PRO A2188 " pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 106.10 25.34 80.76 3.20e+00 9.77e-02 6.37e+02 angle pdb=" CB PRO K 251 " pdb=" CG PRO K 251 " pdb=" CD PRO K 251 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CA PRO A2188 " pdb=" N PRO A2188 " pdb=" CD PRO A2188 " ideal model delta sigma weight residual 112.00 83.27 28.73 1.40e+00 5.10e-01 4.21e+02 angle pdb=" N PRO K 251 " pdb=" CD PRO K 251 " pdb=" CG PRO K 251 " ideal model delta sigma weight residual 103.20 72.61 30.59 1.50e+00 4.44e-01 4.16e+02 angle pdb=" N PRO K 165 " pdb=" CD PRO K 165 " pdb=" CG PRO K 165 " ideal model delta sigma weight residual 103.20 77.96 25.24 1.50e+00 4.44e-01 2.83e+02 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 9619 27.56 - 55.12: 534 55.12 - 82.67: 75 82.67 - 110.23: 7 110.23 - 137.79: 1 Dihedral angle restraints: 10236 sinusoidal: 4695 harmonic: 5541 Sorted by residual: dihedral pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta harmonic sigma weight residual 180.00 125.49 54.51 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLN A 862 " pdb=" C GLN A 862 " pdb=" N TYR A 863 " pdb=" CA TYR A 863 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.62e+01 dihedral pdb=" N PRO A2188 " pdb=" CG PRO A2188 " pdb=" CD PRO A2188 " pdb=" CB PRO A2188 " ideal model delta sinusoidal sigma weight residual -30.00 -167.79 137.79 1 1.50e+01 4.44e-03 7.43e+01 ... (remaining 10233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2367 0.098 - 0.195: 200 0.195 - 0.293: 14 0.293 - 0.390: 13 0.390 - 0.488: 1 Chirality restraints: 2595 Sorted by residual: chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL A 22 " pdb=" CA VAL A 22 " pdb=" CG1 VAL A 22 " pdb=" CG2 VAL A 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 2592 not shown) Planarity restraints: 2767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 250 " 0.113 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO K 251 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO K 251 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO K 251 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 863 " 0.034 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR A 863 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 863 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 863 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 863 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 863 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 863 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 863 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2165 " 0.065 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A2166 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A2166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2166 " 0.056 5.00e-02 4.00e+02 ... (remaining 2764 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 191 2.59 - 3.17: 12857 3.17 - 3.75: 26850 3.75 - 4.32: 35513 4.32 - 4.90: 57564 Nonbonded interactions: 132975 Sorted by model distance: nonbonded pdb=" OD1 ASP A1749 " pdb="MG MG A2301 " model vdw 2.013 2.170 nonbonded pdb=" OP1 C E 39 " pdb="MG MG E 102 " model vdw 2.045 2.170 nonbonded pdb=" OP2 C E 39 " pdb="MG MG E 108 " model vdw 2.050 2.170 nonbonded pdb=" OP2 A E 10 " pdb="MG MG E 105 " model vdw 2.057 2.170 nonbonded pdb=" O ILE A 357 " pdb=" OG SER A 361 " model vdw 2.215 2.440 ... (remaining 132970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic 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: 2.970 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: 18.730 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 52.290 Find NCS groups from input model: 0.450 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 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 : 0.011 0.788 16715 Z= 0.728 Angle : 1.416 80.760 22877 Z= 0.665 Chirality : 0.061 0.488 2595 Planarity : 0.009 0.170 2767 Dihedral : 16.301 137.790 6634 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.95 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.18), residues: 1849 helix: -1.41 (0.16), residues: 810 sheet: -1.94 (0.34), residues: 202 loop : -2.09 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 848 HIS 0.024 0.002 HIS A1896 PHE 0.056 0.003 PHE K 173 TYR 0.070 0.003 TYR A 863 ARG 0.010 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.6776 (p90) cc_final: 0.6014 (p90) REVERT: A 1769 GLU cc_start: 0.6633 (pp20) cc_final: 0.6277 (pp20) REVERT: A 2166 PRO cc_start: 0.7639 (Cg_endo) cc_final: 0.7432 (Cg_exo) REVERT: K 314 MET cc_start: 0.5185 (pmm) cc_final: 0.4533 (pmm) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2974 time to fit residues: 81.1845 Evaluate side-chains 143 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.0000 chunk 112 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1124 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 16715 Z= 0.206 Angle : 0.652 13.998 22877 Z= 0.322 Chirality : 0.040 0.238 2595 Planarity : 0.006 0.142 2767 Dihedral : 13.487 101.960 2845 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.65 % Favored : 93.13 % Rotamer: Outliers : 1.14 % Allowed : 8.37 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1849 helix: -0.31 (0.17), residues: 827 sheet: -2.03 (0.36), residues: 198 loop : -1.88 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 848 HIS 0.007 0.001 HIS A1896 PHE 0.034 0.002 PHE A2171 TYR 0.036 0.001 TYR A 863 ARG 0.006 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7296 (mm110) cc_final: 0.6591 (mm-40) REVERT: A 529 TYR cc_start: 0.6911 (p90) cc_final: 0.5893 (p90) REVERT: A 863 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: A 1769 GLU cc_start: 0.6648 (pp20) cc_final: 0.6253 (pp20) outliers start: 19 outliers final: 8 residues processed: 170 average time/residue: 0.2903 time to fit residues: 74.3462 Evaluate side-chains 153 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.0270 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16715 Z= 0.173 Angle : 0.598 13.671 22877 Z= 0.290 Chirality : 0.039 0.260 2595 Planarity : 0.005 0.126 2767 Dihedral : 13.252 98.910 2845 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.87 % Favored : 92.92 % Rotamer: Outliers : 2.09 % Allowed : 10.94 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.33 (0.19), residues: 1849 helix: 0.24 (0.18), residues: 829 sheet: -1.95 (0.36), residues: 198 loop : -1.75 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 313 HIS 0.006 0.001 HIS A1896 PHE 0.023 0.001 PHE A2171 TYR 0.034 0.001 TYR A 863 ARG 0.012 0.000 ARG A1141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5256 (tt) REVERT: A 53 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 284 ASN cc_start: 0.7033 (OUTLIER) cc_final: 0.6831 (p0) REVERT: A 307 GLN cc_start: 0.7259 (mm110) cc_final: 0.6808 (mm110) REVERT: A 529 TYR cc_start: 0.6909 (p90) cc_final: 0.5802 (p90) REVERT: A 567 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7314 (pt) REVERT: A 863 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: A 1769 GLU cc_start: 0.6571 (pp20) cc_final: 0.6259 (pp20) outliers start: 35 outliers final: 16 residues processed: 183 average time/residue: 0.2975 time to fit residues: 82.0114 Evaluate side-chains 166 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16715 Z= 0.236 Angle : 0.615 11.234 22877 Z= 0.301 Chirality : 0.040 0.254 2595 Planarity : 0.005 0.110 2767 Dihedral : 13.201 100.979 2845 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 2.39 % Allowed : 14.41 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.27 (0.20), residues: 1849 helix: 0.30 (0.18), residues: 828 sheet: -1.94 (0.36), residues: 198 loop : -1.73 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 313 HIS 0.007 0.001 HIS A1896 PHE 0.016 0.002 PHE A1101 TYR 0.036 0.002 TYR A 863 ARG 0.004 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5490 (tt) REVERT: A 53 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: A 231 MET cc_start: 0.5884 (mmt) cc_final: 0.5361 (mmt) REVERT: A 518 ARG cc_start: 0.6988 (mmp80) cc_final: 0.6761 (mmp80) REVERT: A 863 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 1070 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6307 (pp) REVERT: A 1208 TYR cc_start: 0.5617 (p90) cc_final: 0.5121 (p90) REVERT: A 1669 ASP cc_start: 0.4739 (OUTLIER) cc_final: 0.2244 (p0) REVERT: A 1769 GLU cc_start: 0.6656 (pp20) cc_final: 0.6316 (pp20) REVERT: K 258 MET cc_start: 0.3547 (OUTLIER) cc_final: 0.3049 (ppp) REVERT: K 295 MET cc_start: 0.1410 (mmp) cc_final: 0.1074 (mmp) outliers start: 40 outliers final: 24 residues processed: 179 average time/residue: 0.3159 time to fit residues: 86.8576 Evaluate side-chains 171 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 0.0270 chunk 76 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16715 Z= 0.240 Angle : 0.617 14.802 22877 Z= 0.301 Chirality : 0.040 0.246 2595 Planarity : 0.005 0.098 2767 Dihedral : 13.175 102.194 2845 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.84 % Favored : 91.94 % Rotamer: Outliers : 2.57 % Allowed : 15.24 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.19 (0.20), residues: 1849 helix: 0.38 (0.18), residues: 827 sheet: -2.01 (0.37), residues: 188 loop : -1.67 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.006 0.001 HIS A1896 PHE 0.016 0.002 PHE A1552 TYR 0.037 0.001 TYR A 863 ARG 0.004 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5474 (tt) REVERT: A 231 MET cc_start: 0.5945 (mmt) cc_final: 0.5455 (mmt) REVERT: A 343 PHE cc_start: 0.5712 (p90) cc_final: 0.5484 (p90) REVERT: A 518 ARG cc_start: 0.6967 (mmp80) cc_final: 0.6754 (mmp80) REVERT: A 567 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7565 (mt) REVERT: A 863 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: A 1070 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6221 (pp) REVERT: A 1208 TYR cc_start: 0.5668 (p90) cc_final: 0.5158 (p90) REVERT: A 1669 ASP cc_start: 0.4846 (OUTLIER) cc_final: 0.2385 (p0) REVERT: A 1769 GLU cc_start: 0.6696 (pp20) cc_final: 0.6329 (pp20) REVERT: A 1850 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6024 (tp) REVERT: K 258 MET cc_start: 0.3315 (OUTLIER) cc_final: 0.3104 (ptp) REVERT: K 295 MET cc_start: 0.1542 (mmp) cc_final: 0.1209 (mmp) outliers start: 43 outliers final: 29 residues processed: 176 average time/residue: 0.3036 time to fit residues: 82.0550 Evaluate side-chains 176 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16715 Z= 0.161 Angle : 0.570 12.618 22877 Z= 0.277 Chirality : 0.039 0.257 2595 Planarity : 0.004 0.087 2767 Dihedral : 13.069 101.383 2845 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.60 % Favored : 93.19 % Rotamer: Outliers : 2.21 % Allowed : 16.86 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.94 (0.20), residues: 1849 helix: 0.60 (0.18), residues: 835 sheet: -2.00 (0.38), residues: 184 loop : -1.55 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.004 0.001 HIS A1896 PHE 0.013 0.001 PHE A 343 TYR 0.035 0.001 TYR A 863 ARG 0.002 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5171 (tt) REVERT: A 231 MET cc_start: 0.5956 (mmt) cc_final: 0.5517 (mmt) REVERT: A 343 PHE cc_start: 0.5745 (p90) cc_final: 0.5519 (p90) REVERT: A 863 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: A 1070 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6062 (pp) REVERT: A 1208 TYR cc_start: 0.5634 (p90) cc_final: 0.5127 (p90) REVERT: A 1769 GLU cc_start: 0.6528 (pp20) cc_final: 0.6103 (pp20) REVERT: A 1850 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6018 (tp) REVERT: K 258 MET cc_start: 0.3252 (OUTLIER) cc_final: 0.2948 (ppp) REVERT: K 295 MET cc_start: 0.1710 (mmp) cc_final: 0.1408 (mmp) outliers start: 37 outliers final: 21 residues processed: 177 average time/residue: 0.3331 time to fit residues: 90.4815 Evaluate side-chains 164 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 258 MET Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 303 HIS A1067 GLN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2223 ASN K 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16715 Z= 0.327 Angle : 0.672 15.335 22877 Z= 0.331 Chirality : 0.043 0.241 2595 Planarity : 0.005 0.079 2767 Dihedral : 13.108 104.028 2845 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.49 % Favored : 91.29 % Rotamer: Outliers : 2.99 % Allowed : 16.62 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.27 (0.20), residues: 1849 helix: 0.23 (0.18), residues: 837 sheet: -2.03 (0.37), residues: 187 loop : -1.64 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 848 HIS 0.010 0.001 HIS K 360 PHE 0.020 0.002 PHE A1552 TYR 0.039 0.002 TYR A 863 ARG 0.005 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5710 (tt) REVERT: A 191 MET cc_start: 0.8120 (mmt) cc_final: 0.7819 (mmt) REVERT: A 231 MET cc_start: 0.6059 (mmt) cc_final: 0.5564 (mmt) REVERT: A 518 ARG cc_start: 0.6913 (mmp80) cc_final: 0.6693 (mmp80) REVERT: A 567 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7630 (pt) REVERT: A 863 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: A 865 LEU cc_start: 0.7663 (mt) cc_final: 0.7448 (mt) REVERT: A 1070 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6358 (pp) REVERT: A 1208 TYR cc_start: 0.5674 (p90) cc_final: 0.5172 (p90) REVERT: A 1669 ASP cc_start: 0.5124 (OUTLIER) cc_final: 0.2794 (p0) REVERT: A 1769 GLU cc_start: 0.6858 (pp20) cc_final: 0.6405 (pp20) REVERT: A 1850 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.5799 (tp) REVERT: K 295 MET cc_start: 0.1870 (mmp) cc_final: 0.1559 (mmp) outliers start: 50 outliers final: 34 residues processed: 176 average time/residue: 0.2840 time to fit residues: 75.8676 Evaluate side-chains 172 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16715 Z= 0.205 Angle : 0.610 15.004 22877 Z= 0.296 Chirality : 0.040 0.234 2595 Planarity : 0.004 0.068 2767 Dihedral : 13.046 103.872 2845 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.19 % Favored : 92.59 % Rotamer: Outliers : 2.69 % Allowed : 17.99 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.08 (0.20), residues: 1849 helix: 0.43 (0.18), residues: 836 sheet: -1.97 (0.39), residues: 178 loop : -1.60 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 313 HIS 0.006 0.001 HIS A1896 PHE 0.015 0.001 PHE A1552 TYR 0.036 0.001 TYR A 863 ARG 0.003 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5487 (tt) REVERT: A 231 MET cc_start: 0.6082 (mmt) cc_final: 0.5643 (mmt) REVERT: A 343 PHE cc_start: 0.5662 (p90) cc_final: 0.5436 (p90) REVERT: A 518 ARG cc_start: 0.6854 (mmp80) cc_final: 0.6610 (mmp80) REVERT: A 863 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: A 1070 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6421 (pp) REVERT: A 1669 ASP cc_start: 0.4799 (OUTLIER) cc_final: 0.2411 (p0) REVERT: A 1769 GLU cc_start: 0.6747 (pp20) cc_final: 0.6226 (pp20) REVERT: K 312 MET cc_start: 0.0699 (mmm) cc_final: 0.0475 (mmt) REVERT: K 314 MET cc_start: 0.5214 (pmm) cc_final: 0.4892 (pmm) outliers start: 45 outliers final: 29 residues processed: 180 average time/residue: 0.2938 time to fit residues: 81.4561 Evaluate side-chains 170 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1536 ASN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16715 Z= 0.179 Angle : 0.606 16.844 22877 Z= 0.291 Chirality : 0.039 0.204 2595 Planarity : 0.004 0.068 2767 Dihedral : 12.935 102.692 2845 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.75 % Rotamer: Outliers : 2.51 % Allowed : 18.41 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.92 (0.20), residues: 1849 helix: 0.57 (0.18), residues: 833 sheet: -1.94 (0.39), residues: 178 loop : -1.50 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 313 HIS 0.005 0.001 HIS A 303 PHE 0.019 0.001 PHE A 524 TYR 0.032 0.001 TYR A 863 ARG 0.003 0.000 ARG K 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5441 (tt) REVERT: A 191 MET cc_start: 0.8124 (mmm) cc_final: 0.7864 (mmt) REVERT: A 231 MET cc_start: 0.5988 (mmt) cc_final: 0.5566 (mmt) REVERT: A 343 PHE cc_start: 0.5730 (p90) cc_final: 0.5474 (p90) REVERT: A 518 ARG cc_start: 0.6818 (mmp80) cc_final: 0.6600 (mmp80) REVERT: A 863 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6697 (m-80) REVERT: A 935 GLU cc_start: 0.6682 (tt0) cc_final: 0.5959 (mt-10) REVERT: A 1070 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6392 (pp) REVERT: A 1769 GLU cc_start: 0.6663 (pp20) cc_final: 0.6307 (pp20) REVERT: K 295 MET cc_start: 0.1761 (mmp) cc_final: 0.1518 (mmp) REVERT: K 312 MET cc_start: 0.0901 (mmm) cc_final: 0.0694 (mmt) outliers start: 42 outliers final: 35 residues processed: 170 average time/residue: 0.2711 time to fit residues: 71.1074 Evaluate side-chains 172 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 192 optimal weight: 5.9990 chunk 176 optimal weight: 0.0770 chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 118 optimal weight: 0.0980 chunk 93 optimal weight: 0.0020 chunk 121 optimal weight: 0.0770 overall best weight: 0.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1536 ASN ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2223 ASN K 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16715 Z= 0.136 Angle : 0.587 15.907 22877 Z= 0.279 Chirality : 0.038 0.221 2595 Planarity : 0.004 0.067 2767 Dihedral : 12.802 99.222 2845 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.52 % Favored : 94.21 % Rotamer: Outliers : 1.67 % Allowed : 19.37 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.57 (0.20), residues: 1849 helix: 0.87 (0.18), residues: 834 sheet: -1.84 (0.39), residues: 184 loop : -1.30 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 313 HIS 0.004 0.001 HIS A 303 PHE 0.014 0.001 PHE A 343 TYR 0.029 0.001 TYR A 863 ARG 0.003 0.000 ARG K 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5079 (tt) REVERT: A 53 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: A 191 MET cc_start: 0.8045 (mmm) cc_final: 0.7735 (mmt) REVERT: A 343 PHE cc_start: 0.5662 (p90) cc_final: 0.5429 (p90) REVERT: A 518 ARG cc_start: 0.6814 (mmp80) cc_final: 0.6586 (mmp80) REVERT: A 935 GLU cc_start: 0.6579 (tt0) cc_final: 0.5912 (mt-10) REVERT: A 1070 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6270 (pp) REVERT: A 1769 GLU cc_start: 0.6411 (pp20) cc_final: 0.6141 (pp20) REVERT: A 2195 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7331 (mmmt) REVERT: K 295 MET cc_start: 0.2033 (mmp) cc_final: 0.1793 (mmp) outliers start: 28 outliers final: 20 residues processed: 177 average time/residue: 0.2945 time to fit residues: 81.6298 Evaluate side-chains 163 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 202 ASP Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 394 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 141 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 chunk 153 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 HIS ** A1544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.186913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.152631 restraints weight = 27233.922| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 3.15 r_work: 0.4022 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16715 Z= 0.155 Angle : 0.600 16.401 22877 Z= 0.284 Chirality : 0.039 0.184 2595 Planarity : 0.004 0.068 2767 Dihedral : 12.728 98.098 2845 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.95 % Favored : 93.78 % Rotamer: Outliers : 1.61 % Allowed : 19.90 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -0.46 (0.20), residues: 1849 helix: 0.96 (0.18), residues: 830 sheet: -1.85 (0.38), residues: 184 loop : -1.21 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 848 HIS 0.008 0.001 HIS A1174 PHE 0.051 0.002 PHE A 20 TYR 0.023 0.001 TYR A 529 ARG 0.003 0.000 ARG K 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3449.47 seconds wall clock time: 64 minutes 17.53 seconds (3857.53 seconds total)