Starting phenix.real_space_refine on Fri Sep 11 22:34:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rj9_4900/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.map" model { file = "/net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rj9_4900/09_2026/6rj9_4900.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.27, per 1000 atoms: 0.19 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: 0.85 Conformation dependent library (CDL) restraints added in 463.2 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: 1.13 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: 1.84 Time building geometry restraints manager: 1.17 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 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.51e+01 bond pdb=" C1' DC E 12 " pdb=" N1 DC E 12 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.04e+00 bond pdb=" C3' DA E 19 " pdb=" C2' DA E 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.12e+00 bond pdb=" C4' DT E 11 " pdb=" C3' DT E 11 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.39e+00 bond pdb=" C4' DC E 5 " pdb=" C3' DC E 5 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.18e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16542 2.48 - 4.96: 391 4.96 - 7.44: 29 7.44 - 9.92: 3 9.92 - 12.40: 1 Bond angle restraints: 16966 Sorted by residual: angle pdb=" O4' DT E 6 " pdb=" C4' DT E 6 " pdb=" C3' DT E 6 " ideal model delta sigma weight residual 106.00 102.18 3.82 6.00e-01 2.78e+00 4.04e+01 angle pdb=" O4' DC E 5 " pdb=" C4' DC E 5 " pdb=" C3' DC E 5 " ideal model delta sigma weight residual 106.00 102.45 3.55 6.00e-01 2.78e+00 3.51e+01 angle pdb=" O4' DT E 9 " pdb=" C4' DT E 9 " pdb=" C3' DT E 9 " ideal model delta sigma weight residual 106.00 102.67 3.33 6.00e-01 2.78e+00 3.07e+01 angle pdb=" O4' DT E 11 " pdb=" C4' DT E 11 " pdb=" C3' DT E 11 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.41e+01 angle pdb=" O4' DT E 7 " pdb=" C4' DT E 7 " pdb=" C3' DT E 7 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 ... (remaining 16961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6161 17.92 - 35.83: 803 35.83 - 53.75: 198 53.75 - 71.66: 66 71.66 - 89.58: 13 Dihedral angle restraints: 7241 sinusoidal: 3732 harmonic: 3509 Sorted by residual: dihedral pdb=" C4' A D 76 " pdb=" C3' A D 76 " pdb=" C2' A D 76 " pdb=" C1' A D 76 " ideal model delta sinusoidal sigma weight residual 36.34 -38.80 75.14 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' U D 73 " pdb=" C3' U D 73 " pdb=" C2' U D 73 " pdb=" C1' U D 73 " ideal model delta sinusoidal sigma weight residual 36.34 -38.16 74.51 1 3.10e+00 1.04e-01 7.32e+02 dihedral pdb=" C4' U D 8 " pdb=" C3' U D 8 " pdb=" C2' U D 8 " pdb=" C1' U D 8 " ideal model delta sinusoidal sigma weight residual 36.35 -36.46 72.80 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 7238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1569 0.072 - 0.143: 224 0.143 - 0.215: 32 0.215 - 0.286: 60 0.286 - 0.358: 7 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C2' U D 8 " pdb=" C3' U D 8 " pdb=" O2' U D 8 " pdb=" C1' U D 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.43 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C2' U D 73 " pdb=" C3' U D 73 " pdb=" O2' U D 73 " pdb=" C1' U D 73 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2' C D 86 " pdb=" C3' C D 86 " pdb=" O2' C D 86 " pdb=" C1' C D 86 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (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: 1.550 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.430 Find NCS groups from input model: 0.060 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 0.070 12293 Z= 0.311 Angle : 0.869 12.396 16966 Z= 0.473 Chirality : 0.070 0.358 1892 Planarity : 0.006 0.055 1823 Dihedral : 16.937 89.577 4993 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/Z covalent geometry : bond 0.00601 / 0.31 (12293) covalent geometry : angle 0.86894 / 0.47 (16966) hydrogen bonds : bond 0.15553 / 9.57 ( 475) hydrogen bonds : angle 6.54938 / 4.55 ( 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 : 0.341 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: 0.1007 time to fit residues: 28.2123 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 : 0.339 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 43 ASN B 151 GLN B 177 ASN C 21 ASN C 85 ASN C 115 HIS C 276 GLN C 282 ASN C 303 GLN C 696 ASN C 880 GLN C1108 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119264 restraints weight = 16037.042| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.77 r_work: 0.3024 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12293 Z= 0.152 Angle : 0.903 18.046 16966 Z= 0.399 Chirality : 0.084 1.190 1892 Planarity : 0.004 0.040 1823 Dihedral : 13.121 121.123 2475 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.22 % Allowed : 11.95 % Favored : 86.83 % 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: -2.40 (0.21), residues: 1182 helix: -0.77 (0.22), residues: 503 sheet: -0.54 (0.45), residues: 122 loop : -2.66 (0.20), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.020 0.001 TYR A 26 PHE 0.011 0.001 PHE C1042 TRP 0.009 0.001 TRP B 38 HIS 0.003 0.001 HIS C 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (12293) covalent geometry : angle 0.90282 / 0.40 (16966) hydrogen bonds : bond 0.05172 / 3.25 ( 475) hydrogen bonds : angle 4.96829 / 3.48 ( 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 178 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 61 ASP cc_start: 0.8021 (t0) cc_final: 0.7752 (t0) REVERT: B 174 TRP cc_start: 0.6981 (t60) cc_final: 0.6514 (t-100) REVERT: B 181 ASN cc_start: 0.6637 (t0) cc_final: 0.6270 (t0) REVERT: C 41 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 441 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: C 1066 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6352 (t80) outliers start: 13 outliers final: 8 residues processed: 172 average time/residue: 0.1089 time to fit residues: 27.0372 Evaluate side-chains 160 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LEU 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 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: 9.9990 chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 21 ASN C 29 HIS C 61 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 = 0.147988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117077 restraints weight = 16234.264| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.82 r_work: 0.2973 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12293 Z= 0.215 Angle : 0.799 14.827 16966 Z= 0.367 Chirality : 0.065 0.791 1892 Planarity : 0.004 0.039 1823 Dihedral : 12.967 141.905 2475 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.35 % Allowed : 13.08 % Favored : 84.57 % 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: -1.68 (0.23), residues: 1182 helix: 0.07 (0.23), residues: 489 sheet: -0.45 (0.45), residues: 130 loop : -2.43 (0.21), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 966 TYR 0.023 0.002 TYR A 26 PHE 0.013 0.002 PHE C1042 TRP 0.008 0.001 TRP C 726 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (12293) covalent geometry : angle 0.79861 / 0.37 (16966) hydrogen bonds : bond 0.05771 / 3.65 ( 475) hydrogen bonds : angle 4.68829 / 3.28 ( 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 174 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.423 Fit side-chains REVERT: B 13 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 61 ASP cc_start: 0.8114 (t0) cc_final: 0.7836 (t0) REVERT: B 181 ASN cc_start: 0.6703 (t0) cc_final: 0.6343 (t0) REVERT: C 41 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7654 (mm-30) REVERT: C 441 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: C 1066 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6432 (t80) outliers start: 25 outliers final: 18 residues processed: 164 average time/residue: 0.1040 time to fit residues: 25.3400 Evaluate side-chains 160 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 187 SER 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 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 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN C1093 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119860 restraints weight = 16054.675| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.71 r_work: 0.3048 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1606 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= 0.120 Angle : 0.684 14.205 16966 Z= 0.316 Chirality : 0.056 0.593 1892 Planarity : 0.003 0.032 1823 Dihedral : 12.848 136.056 2475 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.16 % Allowed : 13.64 % 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 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: -1.22 (0.23), residues: 1182 helix: 0.56 (0.24), residues: 492 sheet: -0.18 (0.45), residues: 136 loop : -2.33 (0.22), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 385 TYR 0.019 0.001 TYR A 26 PHE 0.009 0.001 PHE B 98 TRP 0.011 0.001 TRP C 726 HIS 0.002 0.001 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (12293) covalent geometry : angle 0.68380 / 0.32 (16966) hydrogen bonds : bond 0.04305 / 2.74 ( 475) hydrogen bonds : angle 4.40401 / 3.09 ( 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 175 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 61 ASP cc_start: 0.8009 (t0) cc_final: 0.7755 (t0) REVERT: B 174 TRP cc_start: 0.7004 (t60) cc_final: 0.6576 (t-100) REVERT: B 181 ASN cc_start: 0.6642 (t0) cc_final: 0.6283 (t0) REVERT: C 41 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7627 (mm-30) REVERT: C 438 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7494 (mm-30) REVERT: C 441 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: C 926 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6866 (mttp) REVERT: C 1064 GLN cc_start: 0.7949 (mp10) cc_final: 0.7684 (mp10) REVERT: C 1066 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6388 (t80) outliers start: 23 outliers final: 11 residues processed: 168 average time/residue: 0.0990 time to fit residues: 24.4870 Evaluate side-chains 163 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 852 ILE Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 1022 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: 8.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 21 ASN C 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115332 restraints weight = 16184.100| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.74 r_work: 0.2973 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12293 Z= 0.250 Angle : 0.778 14.370 16966 Z= 0.361 Chirality : 0.061 0.666 1892 Planarity : 0.004 0.034 1823 Dihedral : 12.847 140.877 2475 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.92 % Allowed : 13.92 % Favored : 83.16 % 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: -1.20 (0.23), residues: 1182 helix: 0.57 (0.24), residues: 490 sheet: -0.46 (0.42), residues: 153 loop : -2.27 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 966 TYR 0.021 0.002 TYR A 26 PHE 0.014 0.002 PHE C1042 TRP 0.007 0.001 TRP C 726 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (12293) covalent geometry : angle 0.77766 / 0.36 (16966) hydrogen bonds : bond 0.05954 / 3.78 ( 475) hydrogen bonds : angle 4.50564 / 3.16 ( 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 174 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 61 ASP cc_start: 0.8088 (t0) cc_final: 0.7847 (t0) REVERT: C 21 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.6094 (t0) REVERT: C 29 HIS cc_start: 0.6577 (t70) cc_final: 0.6324 (t-90) REVERT: C 41 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 438 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 441 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: C 862 MET cc_start: 0.9071 (mmp) cc_final: 0.8862 (mmp) REVERT: C 926 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6784 (mttp) REVERT: C 1066 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.6612 (t80) outliers start: 31 outliers final: 23 residues processed: 162 average time/residue: 0.0960 time to fit residues: 22.8988 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 233 LYS 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 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 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 Chi-restraints excluded: chain C residue 1075 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 43 ASN A 151 GLN C 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116899 restraints weight = 16064.241| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.73 r_work: 0.2992 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1651 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= 0.184 Angle : 0.719 13.589 16966 Z= 0.335 Chirality : 0.057 0.596 1892 Planarity : 0.003 0.033 1823 Dihedral : 12.899 139.761 2475 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.10 % Allowed : 14.68 % Favored : 82.22 % 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: -1.08 (0.23), residues: 1182 helix: 0.72 (0.24), residues: 491 sheet: -0.47 (0.44), residues: 147 loop : -2.22 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 966 TYR 0.023 0.002 TYR C 875 PHE 0.011 0.001 PHE B 98 TRP 0.008 0.001 TRP C 726 HIS 0.002 0.001 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (12293) covalent geometry : angle 0.71884 / 0.33 (16966) hydrogen bonds : bond 0.05204 / 3.30 ( 475) hydrogen bonds : angle 4.41079 / 3.09 ( 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 178 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 61 ASP cc_start: 0.8073 (t0) cc_final: 0.7836 (t0) REVERT: C 41 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 202 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6625 (tm-30) REVERT: C 314 MET cc_start: 0.7928 (tpp) cc_final: 0.7513 (ttt) REVERT: C 438 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 441 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: C 926 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6731 (mttp) REVERT: C 1064 GLN cc_start: 0.8011 (mp10) cc_final: 0.7748 (mp10) REVERT: C 1066 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6644 (t80) outliers start: 33 outliers final: 26 residues processed: 168 average time/residue: 0.1001 time to fit residues: 25.1185 Evaluate side-chains 172 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 148 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 233 LYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 21 ASN C 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118524 restraints weight = 16020.306| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.54 r_work: 0.3038 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1799 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= 0.139 Angle : 0.665 12.572 16966 Z= 0.311 Chirality : 0.054 0.504 1892 Planarity : 0.003 0.030 1823 Dihedral : 12.856 143.323 2475 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.82 % Allowed : 16.09 % 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 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: -0.84 (0.24), residues: 1182 helix: 0.94 (0.24), residues: 491 sheet: -0.26 (0.43), residues: 152 loop : -2.14 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 966 TYR 0.026 0.001 TYR C 875 PHE 0.010 0.001 PHE B 98 TRP 0.013 0.001 TRP C 726 HIS 0.002 0.001 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12293) covalent geometry : angle 0.66510 / 0.31 (16966) hydrogen bonds : bond 0.04574 / 2.92 ( 475) hydrogen bonds : angle 4.28534 / 3.01 ( 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 181 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 61 ASP cc_start: 0.8012 (t0) cc_final: 0.7791 (t0) REVERT: C 314 MET cc_start: 0.7893 (tpp) cc_final: 0.7692 (ttt) REVERT: C 366 GLN cc_start: 0.7684 (mp10) cc_final: 0.7230 (mm110) REVERT: C 438 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7630 (mm-30) REVERT: C 441 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: C 504 ASP cc_start: 0.7183 (m-30) cc_final: 0.6974 (m-30) REVERT: C 926 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6808 (mttp) REVERT: C 1066 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.6626 (t80) outliers start: 30 outliers final: 24 residues processed: 172 average time/residue: 0.0920 time to fit residues: 23.7104 Evaluate side-chains 170 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 43 ASN A 181 ASN C 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114524 restraints weight = 15969.124| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.64 r_work: 0.2971 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12293 Z= 0.286 Angle : 0.793 13.260 16966 Z= 0.370 Chirality : 0.060 0.599 1892 Planarity : 0.004 0.033 1823 Dihedral : 12.906 142.559 2475 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.92 % Allowed : 17.03 % Favored : 80.06 % 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: -0.97 (0.24), residues: 1182 helix: 0.80 (0.24), residues: 490 sheet: -0.31 (0.44), residues: 152 loop : -2.19 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 966 TYR 0.023 0.002 TYR A 26 PHE 0.015 0.002 PHE C1042 TRP 0.010 0.002 TRP C 726 HIS 0.003 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.29 (12293) covalent geometry : angle 0.79297 / 0.37 (16966) hydrogen bonds : bond 0.06150 / 3.93 ( 475) hydrogen bonds : angle 4.47498 / 3.14 ( 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 173 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 61 ASP cc_start: 0.8081 (t0) cc_final: 0.7837 (t0) REVERT: C 314 MET cc_start: 0.7890 (tpp) cc_final: 0.7688 (ttt) REVERT: C 368 ASP cc_start: 0.7404 (t0) cc_final: 0.7146 (t70) REVERT: C 438 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7633 (mp0) REVERT: C 441 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: C 926 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6799 (mttp) REVERT: C 1064 GLN cc_start: 0.8038 (mp10) cc_final: 0.7783 (mp10) REVERT: C 1066 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6735 (t80) outliers start: 31 outliers final: 27 residues processed: 163 average time/residue: 0.0958 time to fit residues: 23.3835 Evaluate side-chains 171 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 148 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 181 ILE 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 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 Chi-restraints excluded: chain C residue 1094 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117826 restraints weight = 15909.003| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.54 r_work: 0.3027 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12293 Z= 0.146 Angle : 0.684 12.210 16966 Z= 0.321 Chirality : 0.054 0.506 1892 Planarity : 0.003 0.029 1823 Dihedral : 12.916 149.658 2475 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.63 % Allowed : 17.59 % Favored : 79.77 % 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: -0.78 (0.24), residues: 1182 helix: 1.01 (0.24), residues: 491 sheet: -0.27 (0.44), residues: 152 loop : -2.12 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 966 TYR 0.021 0.001 TYR C 875 PHE 0.011 0.001 PHE B 98 TRP 0.013 0.001 TRP C 726 HIS 0.002 0.001 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12293) covalent geometry : angle 0.68418 / 0.32 (16966) hydrogen bonds : bond 0.04737 / 3.02 ( 475) hydrogen bonds : angle 4.30659 / 3.02 ( 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 173 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 61 ASP cc_start: 0.8034 (t0) cc_final: 0.7797 (t0) REVERT: C 314 MET cc_start: 0.7910 (tpp) cc_final: 0.7707 (ttt) REVERT: C 438 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7512 (mp0) REVERT: C 441 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: C 926 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6798 (mttp) REVERT: C 1064 GLN cc_start: 0.7949 (mp10) cc_final: 0.7717 (mp10) REVERT: C 1066 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6669 (t80) outliers start: 28 outliers final: 23 residues processed: 164 average time/residue: 0.0837 time to fit residues: 20.6416 Evaluate side-chains 168 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 28 ILE 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 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 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: 4.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116142 restraints weight = 16141.339| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.61 r_work: 0.2991 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1866 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= 0.216 Angle : 0.730 12.373 16966 Z= 0.342 Chirality : 0.056 0.540 1892 Planarity : 0.003 0.031 1823 Dihedral : 12.922 155.058 2475 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.63 % Allowed : 17.87 % 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: -0.81 (0.24), residues: 1182 helix: 0.96 (0.24), residues: 490 sheet: -0.29 (0.44), residues: 152 loop : -2.11 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 966 TYR 0.026 0.002 TYR C 875 PHE 0.012 0.002 PHE C1042 TRP 0.013 0.001 TRP C 726 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (12293) covalent geometry : angle 0.72992 / 0.34 (16966) hydrogen bonds : bond 0.05386 / 3.43 ( 475) hydrogen bonds : angle 4.35585 / 3.05 ( 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 170 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 61 ASP cc_start: 0.8077 (t0) cc_final: 0.7837 (t0) REVERT: C 438 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7519 (mp0) REVERT: C 441 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: C 445 GLU cc_start: 0.5675 (pt0) cc_final: 0.5238 (pt0) REVERT: C 926 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6854 (mttp) REVERT: C 1064 GLN cc_start: 0.7978 (mp10) cc_final: 0.7724 (mp10) REVERT: C 1066 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 28 outliers final: 25 residues processed: 162 average time/residue: 0.1006 time to fit residues: 24.4239 Evaluate side-chains 170 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 148 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 181 ILE 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 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 115 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119347 restraints weight = 16015.325| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.49 r_work: 0.3055 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12293 Z= 0.129 Angle : 0.662 11.401 16966 Z= 0.311 Chirality : 0.052 0.449 1892 Planarity : 0.003 0.030 1823 Dihedral : 12.964 168.436 2475 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.63 % Allowed : 17.87 % 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: -0.65 (0.24), residues: 1182 helix: 1.12 (0.24), residues: 491 sheet: -0.27 (0.44), residues: 152 loop : -2.04 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.024 0.001 TYR C 875 PHE 0.011 0.001 PHE B 98 TRP 0.016 0.001 TRP C 726 HIS 0.002 0.001 HIS C 877 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12293) covalent geometry : angle 0.66234 / 0.31 (16966) hydrogen bonds : bond 0.04330 / 2.77 ( 475) hydrogen bonds : angle 4.20832 / 2.94 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.22 seconds wall clock time: 45 minutes 29.41 seconds (2729.41 seconds total)