Starting phenix.real_space_refine on Wed Mar 4 08:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rj9_4900/03_2026/6rj9_4900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rj9_4900/03_2026/6rj9_4900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rj9_4900/03_2026/6rj9_4900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rj9_4900/03_2026/6rj9_4900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rj9_4900/03_2026/6rj9_4900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rj9_4900/03_2026/6rj9_4900.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 97 5.49 5 S 37 5.16 5 C 7185 2.51 5 N 2050 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11874 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6820 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 815} Chain breaks: 7 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 2.57, per 1000 atoms: 0.22 Number of scatterers: 11874 At special positions: 0 Unit cell: (120.904, 141.351, 110.236, 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 37 16.00 P 97 15.00 O 2505 8.00 N 2050 7.00 C 7185 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=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 508.2 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 45.7% alpha, 12.4% beta 34 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.799A pdb=" N LYS A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.987A pdb=" N ASP A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.653A pdb=" N LYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 87' Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.773A pdb=" N TYR A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'B' and resid 4 through 19 removed outlier: 4.060A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.685A pdb=" N GLN B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.550A pdb=" N MET B 71 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.554A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.625A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.633A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.934A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.715A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.661A pdb=" N GLU C 147 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 148 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.890A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 272 through 284 removed outlier: 3.753A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 310 Processing helix chain 'C' and resid 316 through 327 removed outlier: 3.737A pdb=" N PHE C 320 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.927A pdb=" N ALA C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.777A pdb=" N PHE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.553A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 454 removed outlier: 3.953A pdb=" N ILE C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 479 through 500 removed outlier: 4.109A pdb=" N LYS C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 485 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.636A pdb=" N LEU C 695 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 727 removed outlier: 3.701A pdb=" N THR C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 727 " --> pdb=" O ARG C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 749 removed outlier: 3.955A pdb=" N ASP C 741 " --> pdb=" O HIS C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 868 removed outlier: 4.082A pdb=" N LYS C 867 " --> pdb=" O LYS C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.999A pdb=" N ARG C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 886 Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.642A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.650A pdb=" N MET B 121 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 710 through 713 removed outlier: 3.708A pdb=" N HIS C 29 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS C 30 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER C 811 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 32 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA6, first strand: chain 'C' and resid 934 through 941 removed outlier: 6.606A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.941A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.941A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 967 " --> pdb=" O THR C1022 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR C1022 " --> pdb=" O ALA C 967 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 969 " --> pdb=" O LYS C1020 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB1, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.305A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.36 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: 2303 1.33 - 1.45: 3417 1.45 - 1.57: 6314 1.57 - 1.69: 190 1.69 - 1.82: 69 Bond restraints: 12293 Sorted by residual: bond pdb=" C1' DC E 15 " pdb=" N1 DC E 15 " ideal model delta sigma weight residual 1.490 1.538 -0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CB MET A 152 " pdb=" CG MET A 152 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB ILE C 827 " pdb=" CG2 ILE C 827 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" CB VAL C 957 " pdb=" CG1 VAL C 957 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB ARG A 153 " pdb=" CG ARG A 153 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16694 2.48 - 4.96: 244 4.96 - 7.44: 24 7.44 - 9.92: 3 9.92 - 12.40: 1 Bond angle restraints: 16966 Sorted by residual: angle pdb=" CA LEU C 439 " pdb=" CB LEU C 439 " pdb=" CG LEU C 439 " ideal model delta sigma weight residual 116.30 128.70 -12.40 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C ASN C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.50e+00 angle pdb=" CA TYR A 26 " pdb=" CB TYR A 26 " pdb=" CG TYR A 26 " ideal model delta sigma weight residual 113.90 118.91 -5.01 1.80e+00 3.09e-01 7.74e+00 angle pdb=" CA TYR B 26 " pdb=" CB TYR B 26 " pdb=" CG TYR B 26 " ideal model delta sigma weight residual 113.90 118.67 -4.77 1.80e+00 3.09e-01 7.03e+00 angle pdb=" CA GLU C 887 " pdb=" C GLU C 887 " pdb=" N PRO C 888 " ideal model delta sigma weight residual 118.44 122.65 -4.21 1.59e+00 3.96e-01 7.01e+00 ... (remaining 16961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6369 17.92 - 35.83: 825 35.83 - 53.75: 177 53.75 - 71.66: 96 71.66 - 89.58: 22 Dihedral angle restraints: 7489 sinusoidal: 3980 harmonic: 3509 Sorted by residual: dihedral pdb=" CA GLU C 991 " pdb=" C GLU C 991 " pdb=" N LYS C 992 " pdb=" CA LYS C 992 " ideal model delta harmonic sigma weight residual 180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU C 439 " pdb=" C LEU C 439 " pdb=" N TYR C 440 " pdb=" CA TYR C 440 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR C1036 " pdb=" C THR C1036 " pdb=" N LYS C1037 " pdb=" CA LYS C1037 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1119 0.036 - 0.071: 550 0.071 - 0.107: 152 0.107 - 0.142: 67 0.142 - 0.178: 4 Chirality restraints: 1892 Sorted by residual: chirality pdb=" CB ILE B 164 " pdb=" CA ILE B 164 " pdb=" CG1 ILE B 164 " pdb=" CG2 ILE B 164 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE C 946 " pdb=" N ILE C 946 " pdb=" C ILE C 946 " pdb=" CB ILE C 946 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1889 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 375 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU C 375 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU C 375 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 376 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 376 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C ALA C 376 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA C 376 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR C 377 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C THR C 881 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 881 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE C 882 " -0.016 2.00e-02 2.50e+03 ... (remaining 1820 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3380 2.81 - 3.34: 9192 3.34 - 3.86: 19005 3.86 - 4.38: 22796 4.38 - 4.90: 38223 Nonbonded interactions: 92596 Sorted by model distance: nonbonded pdb=" O ILE C 84 " pdb=" O2' A D 63 " model vdw 2.292 3.040 nonbonded pdb=" OD2 ASP C 968 " pdb=" OH TYR C1004 " model vdw 2.330 3.040 nonbonded pdb=" OG1 THR C1034 " pdb=" O ASN C1093 " model vdw 2.335 3.040 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.336 3.040 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 101 " model vdw 2.345 3.040 ... (remaining 92591 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.006 0.053 12293 Z= 0.261 Angle : 0.783 12.396 16966 Z= 0.421 Chirality : 0.046 0.178 1892 Planarity : 0.006 0.055 1823 Dihedral : 17.392 89.577 5241 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.28 % Allowed : 8.94 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.19), residues: 1182 helix: -2.59 (0.17), residues: 493 sheet: -0.93 (0.45), residues: 122 loop : -2.91 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 413 TYR 0.021 0.002 TYR B 26 PHE 0.030 0.002 PHE C1066 TRP 0.014 0.002 TRP C 726 HIS 0.007 0.002 HIS C 737 Details of bonding type rmsd covalent geometry : bond 0.00579 (12293) covalent geometry : angle 0.78320 (16966) hydrogen bonds : bond 0.15553 ( 475) hydrogen bonds : angle 6.54938 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.8431 (tmm) cc_final: 0.7973 (tmm) REVERT: B 13 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7501 (tm-30) REVERT: B 61 ASP cc_start: 0.7370 (t0) cc_final: 0.7111 (t0) REVERT: B 181 ASN cc_start: 0.6346 (t0) cc_final: 0.6046 (t0) REVERT: C 874 MET cc_start: 0.8174 (ttp) cc_final: 0.7908 (ttm) REVERT: C 1066 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7012 (t80) outliers start: 3 outliers final: 1 residues processed: 195 average time/residue: 0.1127 time to fit residues: 31.3514 Evaluate side-chains 157 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 43 ASN B 151 GLN B 177 ASN C 21 ASN C 85 ASN C 276 GLN C 282 ASN C 303 GLN C 696 ASN C 880 GLN C1039 GLN C1108 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119112 restraints weight = 16033.749| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.70 r_work: 0.3030 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12293 Z= 0.111 Angle : 0.504 7.863 16966 Z= 0.273 Chirality : 0.037 0.135 1892 Planarity : 0.003 0.037 1823 Dihedral : 15.767 74.355 2723 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.41 % Allowed : 11.85 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.22), residues: 1182 helix: -0.53 (0.22), residues: 493 sheet: -0.60 (0.44), residues: 130 loop : -2.53 (0.21), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 385 TYR 0.022 0.001 TYR A 26 PHE 0.009 0.001 PHE A 33 TRP 0.010 0.001 TRP C 726 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00234 (12293) covalent geometry : angle 0.50425 (16966) hydrogen bonds : bond 0.04520 ( 475) hydrogen bonds : angle 4.68547 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.406 Fit side-chains REVERT: B 13 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 61 ASP cc_start: 0.8056 (t0) cc_final: 0.7811 (t0) REVERT: B 174 TRP cc_start: 0.6875 (t60) cc_final: 0.6503 (t-100) REVERT: B 181 ASN cc_start: 0.6582 (t0) cc_final: 0.6230 (t0) REVERT: C 441 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: C 445 GLU cc_start: 0.5634 (pt0) cc_final: 0.5143 (pt0) REVERT: C 1066 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6574 (t80) outliers start: 15 outliers final: 10 residues processed: 175 average time/residue: 0.1132 time to fit residues: 28.4856 Evaluate side-chains 164 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 21 ASN C 29 HIS C 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115588 restraints weight = 16213.781| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.10 r_work: 0.2965 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12293 Z= 0.183 Angle : 0.550 9.012 16966 Z= 0.292 Chirality : 0.039 0.139 1892 Planarity : 0.003 0.038 1823 Dihedral : 15.693 74.423 2723 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.07 % Allowed : 13.08 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1182 helix: 0.25 (0.24), residues: 490 sheet: -0.34 (0.45), residues: 130 loop : -2.33 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 966 TYR 0.022 0.002 TYR A 26 PHE 0.011 0.001 PHE C1042 TRP 0.009 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00416 (12293) covalent geometry : angle 0.54975 (16966) hydrogen bonds : bond 0.05271 ( 475) hydrogen bonds : angle 4.50259 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 181 ASN cc_start: 0.6657 (t0) cc_final: 0.6265 (t0) REVERT: C 29 HIS cc_start: 0.6602 (t70) cc_final: 0.6354 (t-90) REVERT: C 140 LYS cc_start: 0.8036 (mttp) cc_final: 0.7833 (mtpp) REVERT: C 441 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: C 1066 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6557 (t80) outliers start: 22 outliers final: 16 residues processed: 162 average time/residue: 0.1053 time to fit residues: 25.0461 Evaluate side-chains 162 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 12 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 43 ASN B 151 GLN C1093 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121990 restraints weight = 16035.541| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.78 r_work: 0.3069 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12293 Z= 0.086 Angle : 0.446 7.538 16966 Z= 0.240 Chirality : 0.035 0.133 1892 Planarity : 0.003 0.032 1823 Dihedral : 15.504 74.270 2723 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.26 % Allowed : 13.73 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.24), residues: 1182 helix: 0.81 (0.24), residues: 496 sheet: -0.39 (0.41), residues: 162 loop : -2.20 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 385 TYR 0.020 0.001 TYR C 875 PHE 0.008 0.001 PHE A 33 TRP 0.010 0.001 TRP C 726 HIS 0.002 0.001 HIS C 877 Details of bonding type rmsd covalent geometry : bond 0.00179 (12293) covalent geometry : angle 0.44629 (16966) hydrogen bonds : bond 0.03455 ( 475) hydrogen bonds : angle 4.03135 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 174 TRP cc_start: 0.7052 (t60) cc_final: 0.6673 (t-100) REVERT: B 181 ASN cc_start: 0.6674 (t0) cc_final: 0.6319 (t0) REVERT: C 411 GLN cc_start: 0.7215 (pp30) cc_final: 0.6986 (pp30) REVERT: C 438 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7633 (mm-30) REVERT: C 441 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: C 487 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8065 (mmm-85) REVERT: C 844 TYR cc_start: 0.8973 (m-80) cc_final: 0.8729 (m-80) REVERT: C 926 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6766 (mttp) REVERT: C 1064 GLN cc_start: 0.7838 (mp10) cc_final: 0.7572 (mp10) REVERT: C 1066 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6673 (t80) outliers start: 24 outliers final: 13 residues processed: 189 average time/residue: 0.1044 time to fit residues: 28.8851 Evaluate side-chains 175 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 0.0020 chunk 65 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 21 ASN C 29 HIS C 705 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115582 restraints weight = 16155.611| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.83 r_work: 0.2984 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12293 Z= 0.177 Angle : 0.531 7.390 16966 Z= 0.281 Chirality : 0.039 0.142 1892 Planarity : 0.003 0.033 1823 Dihedral : 15.512 74.355 2723 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.63 % Allowed : 15.99 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.24), residues: 1182 helix: 0.97 (0.24), residues: 488 sheet: -0.25 (0.43), residues: 152 loop : -2.16 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 966 TYR 0.019 0.002 TYR A 26 PHE 0.011 0.001 PHE C1042 TRP 0.009 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00403 (12293) covalent geometry : angle 0.53074 (16966) hydrogen bonds : bond 0.04996 ( 475) hydrogen bonds : angle 4.22956 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.411 Fit side-chains REVERT: A 113 ASP cc_start: 0.8721 (t0) cc_final: 0.8514 (t0) REVERT: B 13 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 78 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8315 (m110) REVERT: C 21 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6275 (t0) REVERT: C 29 HIS cc_start: 0.6638 (t70) cc_final: 0.6373 (t-90) REVERT: C 441 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: C 487 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.8112 (mmm-85) REVERT: C 1066 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6796 (t80) outliers start: 28 outliers final: 22 residues processed: 172 average time/residue: 0.1015 time to fit residues: 26.1324 Evaluate side-chains 173 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1094 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 18 optimal weight: 0.0030 chunk 42 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115580 restraints weight = 16114.654| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.79 r_work: 0.2969 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12293 Z= 0.218 Angle : 0.569 7.445 16966 Z= 0.301 Chirality : 0.040 0.140 1892 Planarity : 0.003 0.031 1823 Dihedral : 15.589 74.451 2723 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.01 % Allowed : 15.99 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1182 helix: 0.89 (0.24), residues: 490 sheet: -0.23 (0.43), residues: 152 loop : -2.15 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 966 TYR 0.021 0.002 TYR A 26 PHE 0.013 0.002 PHE C1042 TRP 0.008 0.001 TRP C 726 HIS 0.003 0.001 HIS C 877 Details of bonding type rmsd covalent geometry : bond 0.00497 (12293) covalent geometry : angle 0.56868 (16966) hydrogen bonds : bond 0.05554 ( 475) hydrogen bonds : angle 4.36331 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.419 Fit side-chains REVERT: A 113 ASP cc_start: 0.8756 (t0) cc_final: 0.8503 (t0) REVERT: B 13 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 78 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8274 (m110) REVERT: B 139 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8735 (mt-10) REVERT: C 21 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6371 (t0) REVERT: C 441 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: C 487 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8162 (mmm-85) REVERT: C 1064 GLN cc_start: 0.7969 (mp10) cc_final: 0.7731 (mp10) REVERT: C 1066 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6862 (t80) outliers start: 32 outliers final: 24 residues processed: 166 average time/residue: 0.0968 time to fit residues: 23.9503 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1094 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119522 restraints weight = 16039.585| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.70 r_work: 0.3035 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12293 Z= 0.102 Angle : 0.471 6.863 16966 Z= 0.251 Chirality : 0.036 0.138 1892 Planarity : 0.003 0.029 1823 Dihedral : 15.502 74.388 2723 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.82 % Allowed : 16.65 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1182 helix: 1.26 (0.24), residues: 492 sheet: -0.40 (0.41), residues: 162 loop : -2.02 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.016 0.001 TYR A 26 PHE 0.009 0.001 PHE B 98 TRP 0.011 0.001 TRP C 726 HIS 0.003 0.001 HIS C 877 Details of bonding type rmsd covalent geometry : bond 0.00219 (12293) covalent geometry : angle 0.47122 (16966) hydrogen bonds : bond 0.03876 ( 475) hydrogen bonds : angle 4.04237 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.428 Fit side-chains REVERT: A 113 ASP cc_start: 0.8702 (t0) cc_final: 0.8462 (t0) REVERT: B 13 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 174 TRP cc_start: 0.7089 (t60) cc_final: 0.6588 (t-100) REVERT: C 29 HIS cc_start: 0.6680 (t70) cc_final: 0.6478 (t-90) REVERT: C 441 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: C 487 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.8178 (mmm-85) REVERT: C 926 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6894 (mttp) REVERT: C 1064 GLN cc_start: 0.7875 (mp10) cc_final: 0.7641 (mp10) REVERT: C 1066 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6839 (t80) outliers start: 30 outliers final: 19 residues processed: 178 average time/residue: 0.0993 time to fit residues: 25.6085 Evaluate side-chains 171 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118589 restraints weight = 15993.102| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.70 r_work: 0.3008 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12293 Z= 0.142 Angle : 0.502 7.500 16966 Z= 0.266 Chirality : 0.038 0.140 1892 Planarity : 0.003 0.030 1823 Dihedral : 15.493 74.406 2723 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.26 % Allowed : 17.59 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1182 helix: 1.28 (0.24), residues: 491 sheet: -0.22 (0.43), residues: 152 loop : -2.02 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.017 0.001 TYR A 26 PHE 0.010 0.001 PHE B 98 TRP 0.010 0.001 TRP C 726 HIS 0.003 0.001 HIS C 877 Details of bonding type rmsd covalent geometry : bond 0.00319 (12293) covalent geometry : angle 0.50207 (16966) hydrogen bonds : bond 0.04471 ( 475) hydrogen bonds : angle 4.08003 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8761 (t0) cc_final: 0.8530 (t0) REVERT: B 13 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 29 HIS cc_start: 0.6715 (t70) cc_final: 0.6477 (t-90) REVERT: C 441 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: C 926 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6956 (mttp) REVERT: C 1066 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6893 (t80) outliers start: 24 outliers final: 20 residues processed: 168 average time/residue: 0.0917 time to fit residues: 23.0091 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 4 optimal weight: 0.8980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119041 restraints weight = 15957.338| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.75 r_work: 0.3033 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12293 Z= 0.113 Angle : 0.476 7.536 16966 Z= 0.253 Chirality : 0.036 0.136 1892 Planarity : 0.003 0.029 1823 Dihedral : 15.468 74.360 2723 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.45 % Allowed : 17.59 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1182 helix: 1.41 (0.24), residues: 491 sheet: -0.33 (0.42), residues: 162 loop : -1.96 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.016 0.001 TYR A 26 PHE 0.010 0.001 PHE B 98 TRP 0.012 0.001 TRP C 726 HIS 0.003 0.001 HIS C 877 Details of bonding type rmsd covalent geometry : bond 0.00249 (12293) covalent geometry : angle 0.47612 (16966) hydrogen bonds : bond 0.03937 ( 475) hydrogen bonds : angle 3.97761 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8748 (t0) cc_final: 0.8536 (t0) REVERT: B 13 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 174 TRP cc_start: 0.7113 (t60) cc_final: 0.6615 (t-100) REVERT: C 29 HIS cc_start: 0.6703 (t70) cc_final: 0.6462 (t-90) REVERT: C 441 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7190 (pm20) REVERT: C 844 TYR cc_start: 0.8956 (m-80) cc_final: 0.8735 (m-80) REVERT: C 926 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6936 (mttp) REVERT: C 1066 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6852 (t80) outliers start: 26 outliers final: 21 residues processed: 173 average time/residue: 0.0929 time to fit residues: 23.9901 Evaluate side-chains 172 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.0000 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 0.0010 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 overall best weight: 0.2828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 178 HIS C 348 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125285 restraints weight = 16246.760| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.56 r_work: 0.3143 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12293 Z= 0.086 Angle : 0.443 7.663 16966 Z= 0.236 Chirality : 0.035 0.139 1892 Planarity : 0.002 0.027 1823 Dihedral : 15.415 74.180 2723 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.69 % Allowed : 18.81 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1182 helix: 1.67 (0.24), residues: 490 sheet: -0.32 (0.41), residues: 165 loop : -1.84 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.015 0.001 TYR A 26 PHE 0.009 0.001 PHE C 211 TRP 0.009 0.001 TRP C 726 HIS 0.002 0.001 HIS C 701 Details of bonding type rmsd covalent geometry : bond 0.00181 (12293) covalent geometry : angle 0.44326 (16966) hydrogen bonds : bond 0.02996 ( 475) hydrogen bonds : angle 3.69475 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 51 MET cc_start: 0.8811 (mtt) cc_final: 0.8599 (mtp) REVERT: B 174 TRP cc_start: 0.7095 (t60) cc_final: 0.6728 (t-100) REVERT: C 705 HIS cc_start: 0.6687 (m-70) cc_final: 0.6387 (m-70) REVERT: C 940 SER cc_start: 0.8982 (p) cc_final: 0.8486 (m) REVERT: C 1066 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.6873 (t80) outliers start: 18 outliers final: 11 residues processed: 175 average time/residue: 0.1018 time to fit residues: 26.0304 Evaluate side-chains 162 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1066 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 115 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 HIS C 178 HIS C 880 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123003 restraints weight = 15999.948| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.40 r_work: 0.3132 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12293 Z= 0.093 Angle : 0.457 7.693 16966 Z= 0.242 Chirality : 0.035 0.130 1892 Planarity : 0.002 0.031 1823 Dihedral : 15.336 74.095 2723 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.13 % Allowed : 19.00 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1182 helix: 1.78 (0.24), residues: 490 sheet: -0.26 (0.41), residues: 165 loop : -1.77 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.020 0.001 TYR C1061 PHE 0.008 0.001 PHE C1121 TRP 0.012 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00203 (12293) covalent geometry : angle 0.45669 (16966) hydrogen bonds : bond 0.03299 ( 475) hydrogen bonds : angle 3.70714 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.62 seconds wall clock time: 47 minutes 54.76 seconds (2874.76 seconds total)