Starting phenix.real_space_refine on Wed Jul 30 05:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rj9_4900/07_2025/6rj9_4900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rj9_4900/07_2025/6rj9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6rj9_4900/07_2025/6rj9_4900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rj9_4900/07_2025/6rj9_4900.map" model { file = "/net/cci-nas-00/data/ceres_data/6rj9_4900/07_2025/6rj9_4900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rj9_4900/07_2025/6rj9_4900.cif" } resolution = 3.2 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= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.98, per 1000 atoms: 0.67 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.91 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: 4.60 Time building geometry restraints manager: 3.29 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: 1.530 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.014 0.002 TRP C 726 HIS 0.007 0.002 HIS C 737 PHE 0.030 0.002 PHE C1066 TYR 0.021 0.002 TYR B 26 ARG 0.005 0.001 ARG C 413 Details of bonding type rmsd hydrogen bonds : bond 0.15553 ( 475) hydrogen bonds : angle 6.54938 ( 1308) covalent geometry : bond 0.00579 (12293) covalent geometry : angle 0.78320 (16966) *********************** 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 : 1.133 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: 0.7112 (t0) REVERT: B 181 ASN cc_start: 0.6345 (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: 0.2520 time to fit residues: 69.4290 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 : 1.113 ------------------------------------------------------------------------------- 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 107 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.152330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120172 restraints weight = 15942.258| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.87 r_work: 0.3050 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12293 Z= 0.101 Angle : 0.487 8.095 16966 Z= 0.264 Chirality : 0.036 0.136 1892 Planarity : 0.003 0.036 1823 Dihedral : 15.728 74.377 2723 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.51 % Allowed : 11.95 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.22), residues: 1182 helix: -0.51 (0.22), residues: 494 sheet: -0.49 (0.44), residues: 136 loop : -2.54 (0.21), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 726 HIS 0.002 0.000 HIS C 61 PHE 0.009 0.001 PHE A 33 TYR 0.023 0.001 TYR A 26 ARG 0.003 0.000 ARG C 385 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 475) hydrogen bonds : angle 4.56470 ( 1308) covalent geometry : bond 0.00211 (12293) covalent geometry : angle 0.48686 (16966) *********************** 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 191 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 61 ASP cc_start: 0.8063 (t0) cc_final: 0.7807 (t0) REVERT: B 181 ASN cc_start: 0.6564 (t0) cc_final: 0.6211 (t0) REVERT: C 41 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7600 (mm-30) REVERT: C 441 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: C 445 GLU cc_start: 0.5639 (pt0) cc_final: 0.5169 (pt0) REVERT: C 1066 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6574 (t80) outliers start: 16 outliers final: 11 residues processed: 185 average time/residue: 0.2454 time to fit residues: 64.7675 Evaluate side-chains 164 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER 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 69 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 44 optimal weight: 0.0170 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.7224 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.147580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114880 restraints weight = 16227.510| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.86 r_work: 0.2974 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12293 Z= 0.204 Angle : 0.563 9.341 16966 Z= 0.299 Chirality : 0.040 0.144 1892 Planarity : 0.003 0.036 1823 Dihedral : 15.685 74.417 2723 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.35 % Allowed : 13.45 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1182 helix: 0.28 (0.24), residues: 491 sheet: -0.31 (0.46), residues: 130 loop : -2.35 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 174 HIS 0.003 0.001 HIS C 61 PHE 0.012 0.002 PHE C1042 TYR 0.022 0.002 TYR A 26 ARG 0.004 0.000 ARG C 966 Details of bonding type rmsd hydrogen bonds : bond 0.05502 ( 475) hydrogen bonds : angle 4.50631 ( 1308) covalent geometry : bond 0.00465 (12293) covalent geometry : angle 0.56307 (16966) *********************** 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 174 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.114 Fit side-chains REVERT: B 13 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 181 ASN cc_start: 0.6740 (t0) cc_final: 0.6358 (t0) REVERT: C 29 HIS cc_start: 0.6595 (t70) cc_final: 0.6378 (t-90) REVERT: C 41 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 68 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7991 (ttm170) REVERT: C 441 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: C 1066 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6583 (t80) outliers start: 25 outliers final: 18 residues processed: 163 average time/residue: 0.2331 time to fit residues: 55.7523 Evaluate side-chains 163 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 176 GLU 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 249 ASP 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 Chi-restraints excluded: chain C residue 1094 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 chunk 59 optimal weight: 0.0170 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 30 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4014 ------------------------------------------------------------------------------- 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 A 151 GLN C 348 HIS C1093 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121771 restraints weight = 15927.135| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.73 r_work: 0.3086 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12293 Z= 0.086 Angle : 0.447 7.858 16966 Z= 0.239 Chirality : 0.035 0.134 1892 Planarity : 0.003 0.030 1823 Dihedral : 15.499 74.238 2723 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.88 % Allowed : 14.49 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1182 helix: 0.88 (0.24), residues: 496 sheet: -0.40 (0.41), residues: 162 loop : -2.15 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 726 HIS 0.003 0.001 HIS C 115 PHE 0.008 0.001 PHE A 33 TYR 0.021 0.001 TYR C 875 ARG 0.002 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 475) hydrogen bonds : angle 4.00630 ( 1308) covalent geometry : bond 0.00177 (12293) covalent geometry : angle 0.44667 (16966) *********************** 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 188 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 181 ASN cc_start: 0.6672 (t0) cc_final: 0.6310 (t0) REVERT: C 68 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7822 (ttm170) REVERT: C 438 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7614 (mm-30) REVERT: C 441 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: C 487 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.8032 (mmm-85) REVERT: C 926 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6754 (mttp) REVERT: C 1066 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6645 (t80) outliers start: 20 outliers final: 12 residues processed: 180 average time/residue: 0.2359 time to fit residues: 61.6639 Evaluate side-chains 166 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 MET 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 695 LEU Chi-restraints excluded: chain C residue 843 THR 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 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1094 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 21 ASN C 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116142 restraints weight = 16071.430| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.85 r_work: 0.3005 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1763 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= 0.163 Angle : 0.510 7.358 16966 Z= 0.271 Chirality : 0.038 0.141 1892 Planarity : 0.003 0.033 1823 Dihedral : 15.482 74.326 2723 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.10 % Allowed : 14.96 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1182 helix: 1.07 (0.24), residues: 489 sheet: -0.29 (0.43), residues: 153 loop : -2.11 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 PHE 0.010 0.001 PHE B 98 TYR 0.018 0.001 TYR A 26 ARG 0.003 0.000 ARG C 966 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 475) hydrogen bonds : angle 4.13215 ( 1308) covalent geometry : bond 0.00372 (12293) covalent geometry : angle 0.50956 (16966) *********************** 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 184 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8695 (t0) cc_final: 0.8486 (t0) REVERT: B 13 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 78 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8368 (m110) REVERT: B 181 ASN cc_start: 0.6737 (t0) cc_final: 0.6357 (t0) REVERT: C 441 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: C 487 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.8115 (mmm-85) REVERT: C 1066 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6748 (t80) outliers start: 33 outliers final: 22 residues processed: 172 average time/residue: 0.2218 time to fit residues: 56.4049 Evaluate side-chains 170 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 28 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 249 ASP 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 1066 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.151566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119526 restraints weight = 16140.555| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.80 r_work: 0.3040 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12293 Z= 0.105 Angle : 0.463 7.073 16966 Z= 0.247 Chirality : 0.036 0.135 1892 Planarity : 0.003 0.030 1823 Dihedral : 15.444 74.291 2723 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.26 % Allowed : 16.46 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1182 helix: 1.28 (0.24), residues: 489 sheet: -0.37 (0.41), residues: 162 loop : -2.00 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 PHE 0.008 0.001 PHE B 98 TYR 0.016 0.001 TYR A 26 ARG 0.001 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 475) hydrogen bonds : angle 3.94789 ( 1308) covalent geometry : bond 0.00231 (12293) covalent geometry : angle 0.46301 (16966) *********************** 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 173 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8704 (t0) cc_final: 0.8478 (t0) REVERT: B 13 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 181 ASN cc_start: 0.6708 (t0) cc_final: 0.6342 (t0) REVERT: C 441 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: C 487 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8139 (mmm-85) REVERT: C 844 TYR cc_start: 0.8975 (m-80) cc_final: 0.8758 (m-80) REVERT: C 926 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6795 (mttp) REVERT: C 1066 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.6814 (t80) outliers start: 24 outliers final: 18 residues processed: 166 average time/residue: 0.2288 time to fit residues: 55.8534 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 249 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 926 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.149407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117591 restraints weight = 16195.128| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.77 r_work: 0.3002 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 0.026 12293 Z= 0.151 Angle : 0.500 7.061 16966 Z= 0.267 Chirality : 0.038 0.137 1892 Planarity : 0.003 0.030 1823 Dihedral : 15.460 74.338 2723 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.63 % Allowed : 16.27 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1182 helix: 1.28 (0.24), residues: 489 sheet: -0.23 (0.43), residues: 152 loop : -2.02 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 PHE 0.010 0.001 PHE C1042 TYR 0.017 0.001 TYR A 26 ARG 0.003 0.000 ARG C 966 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 475) hydrogen bonds : angle 4.04257 ( 1308) covalent geometry : bond 0.00342 (12293) covalent geometry : angle 0.49987 (16966) *********************** 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 175 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.114 Fit side-chains REVERT: A 113 ASP cc_start: 0.8754 (t0) cc_final: 0.8520 (t0) REVERT: B 13 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 21 ASN cc_start: 0.6312 (OUTLIER) cc_final: 0.6060 (t0) REVERT: C 441 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: C 487 ARG cc_start: 0.8394 (mtp-110) cc_final: 0.8188 (mmm-85) REVERT: C 844 TYR cc_start: 0.8975 (m-80) cc_final: 0.8748 (m-80) outliers start: 28 outliers final: 23 residues processed: 169 average time/residue: 0.2194 time to fit residues: 54.7747 Evaluate side-chains 169 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 21 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 249 ASP 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 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 76 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 112 optimal weight: 0.1980 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.153919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121706 restraints weight = 16157.345| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.61 r_work: 0.3099 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12293 Z= 0.088 Angle : 0.448 6.808 16966 Z= 0.239 Chirality : 0.035 0.135 1892 Planarity : 0.002 0.027 1823 Dihedral : 15.420 74.271 2723 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 17.22 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1182 helix: 1.50 (0.24), residues: 492 sheet: -0.36 (0.41), residues: 162 loop : -1.88 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 726 HIS 0.003 0.001 HIS C 877 PHE 0.008 0.001 PHE C 278 TYR 0.015 0.001 TYR A 26 ARG 0.001 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 475) hydrogen bonds : angle 3.81003 ( 1308) covalent geometry : bond 0.00184 (12293) covalent geometry : angle 0.44819 (16966) *********************** 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 180 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 441 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: C 844 TYR cc_start: 0.8887 (m-80) cc_final: 0.8617 (m-80) REVERT: C 926 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6893 (mttp) REVERT: C 1066 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6690 (t80) outliers start: 20 outliers final: 15 residues processed: 172 average time/residue: 0.3195 time to fit residues: 82.0164 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121534 restraints weight = 16058.431| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.36 r_work: 0.3102 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12293 Z= 0.100 Angle : 0.460 6.782 16966 Z= 0.246 Chirality : 0.036 0.132 1892 Planarity : 0.002 0.029 1823 Dihedral : 15.380 74.211 2723 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 17.78 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1182 helix: 1.58 (0.24), residues: 492 sheet: -0.28 (0.42), residues: 162 loop : -1.82 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 PHE 0.008 0.001 PHE B 98 TYR 0.016 0.001 TYR A 26 ARG 0.003 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 475) hydrogen bonds : angle 3.78271 ( 1308) covalent geometry : bond 0.00218 (12293) covalent geometry : angle 0.46021 (16966) *********************** 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 172 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 844 TYR cc_start: 0.8857 (m-80) cc_final: 0.8615 (m-80) outliers start: 21 outliers final: 19 residues processed: 165 average time/residue: 0.3126 time to fit residues: 75.4701 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 164 ILE 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 440 TYR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.147524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116128 restraints weight = 15990.926| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.69 r_work: 0.2976 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12293 Z= 0.218 Angle : 0.571 7.957 16966 Z= 0.302 Chirality : 0.040 0.145 1892 Planarity : 0.003 0.028 1823 Dihedral : 15.509 74.378 2723 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.16 % Allowed : 17.87 % 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 (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: -0.45 (0.24), residues: 1182 helix: 1.33 (0.24), residues: 490 sheet: -0.14 (0.44), residues: 152 loop : -1.97 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 726 HIS 0.003 0.001 HIS C 877 PHE 0.015 0.002 PHE A 41 TYR 0.020 0.002 TYR A 26 ARG 0.005 0.000 ARG C 235 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 475) hydrogen bonds : angle 4.17417 ( 1308) covalent geometry : bond 0.00498 (12293) covalent geometry : angle 0.57100 (16966) ********************** 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 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 926 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6754 (mttp) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 0.2256 time to fit residues: 53.8291 Evaluate side-chains 159 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 121 MET 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 331 VAL Chi-restraints excluded: chain C residue 402 SER 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 843 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 104 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120199 restraints weight = 15995.067| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.63 r_work: 0.3053 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2133 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= 0.110 Angle : 0.485 7.708 16966 Z= 0.258 Chirality : 0.036 0.139 1892 Planarity : 0.003 0.027 1823 Dihedral : 15.444 74.374 2723 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.60 % Allowed : 18.44 % 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 (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: -0.24 (0.24), residues: 1182 helix: 1.58 (0.24), residues: 491 sheet: -0.32 (0.42), residues: 162 loop : -1.88 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 PHE 0.008 0.001 PHE C1042 TYR 0.018 0.001 TYR C1061 ARG 0.003 0.000 ARG C 235 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 475) hydrogen bonds : angle 3.91184 ( 1308) covalent geometry : bond 0.00244 (12293) covalent geometry : angle 0.48453 (16966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6308.43 seconds wall clock time: 111 minutes 47.44 seconds (6707.44 seconds total)