Starting phenix.real_space_refine on Sat Jul 4 01:21:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m48_63618/07_2026/9m48_63618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m48_63618/07_2026/9m48_63618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m48_63618/07_2026/9m48_63618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m48_63618/07_2026/9m48_63618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m48_63618/07_2026/9m48_63618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m48_63618/07_2026/9m48_63618.map" } resolution = 2.6 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Co 1 6.85 5 P 62 5.49 5 S 56 5.16 5 C 10661 2.51 5 N 2770 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16978 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain: "B" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2705 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "C" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "D" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2091 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 2 Chain: "E" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "G" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CO': 1} Chain breaks: 1 Time building chain proxies: 4.13, per 1000 atoms: 0.24 Number of scatterers: 16978 At special positions: 0 Unit cell: (120.96, 124.32, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 1 26.99 S 56 16.00 P 62 15.00 O 3428 8.00 N 2770 7.00 C 10661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 724.8 milliseconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 43 sheets defined 25.9% alpha, 21.3% beta 30 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.890A pdb=" N VAL F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 298 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.627A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.277A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.144A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 266 removed outlier: 5.084A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 282 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 321 removed outlier: 7.187A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.630A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.253A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.299A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 266 removed outlier: 5.090A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 315 through 322 Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.637A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.222A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AB9, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.198A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AC2, first strand: chain 'C' and resid 264 through 266 removed outlier: 5.208A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.608A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.667A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.277A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC7, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.274A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.761A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AD2, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.659A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.219A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.219A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AD6, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.253A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AD8, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.873A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 315 through 322 Processing sheet with id=AE1, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.611A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.325A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE4, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.256A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AE6, first strand: chain 'F' and resid 264 through 266 removed outlier: 5.021A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 315 through 322 586 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5182 1.34 - 1.45: 2818 1.45 - 1.57: 9243 1.57 - 1.69: 122 1.69 - 1.81: 83 Bond restraints: 17448 Sorted by residual: bond pdb=" C ALA A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.340 1.366 -0.026 2.76e-02 1.31e+03 9.08e-01 bond pdb=" C ALA C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.340 1.366 -0.026 2.76e-02 1.31e+03 8.87e-01 bond pdb=" C ALA B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.340 1.363 -0.023 2.76e-02 1.31e+03 7.13e-01 bond pdb=" CA GLY A 246 " pdb=" C GLY A 246 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 5.93e-01 bond pdb=" CA ASN E 136 " pdb=" CB ASN E 136 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.68e-02 3.54e+03 5.89e-01 ... (remaining 17443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 23739 1.57 - 3.15: 200 3.15 - 4.72: 17 4.72 - 6.29: 1 6.29 - 7.87: 1 Bond angle restraints: 23958 Sorted by residual: angle pdb=" C ALA D 117 " pdb=" N PRO D 118 " pdb=" CA PRO D 118 " ideal model delta sigma weight residual 121.65 118.99 2.66 1.01e+00 9.80e-01 6.95e+00 angle pdb=" N GLY A 246 " pdb=" CA GLY A 246 " pdb=" C GLY A 246 " ideal model delta sigma weight residual 110.71 114.40 -3.69 1.53e+00 4.27e-01 5.81e+00 angle pdb=" O2 C H 35 " pdb=" C2 C H 35 " pdb=" N3 C H 35 " ideal model delta sigma weight residual 121.90 120.31 1.59 7.00e-01 2.04e+00 5.18e+00 angle pdb=" CA LEU B 311 " pdb=" CB LEU B 311 " pdb=" CG LEU B 311 " ideal model delta sigma weight residual 116.30 124.17 -7.87 3.50e+00 8.16e-02 5.05e+00 angle pdb=" C ALA E 117 " pdb=" N PRO E 118 " pdb=" CA PRO E 118 " ideal model delta sigma weight residual 121.91 119.08 2.83 1.35e+00 5.49e-01 4.40e+00 ... (remaining 23953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9352 17.86 - 35.73: 779 35.73 - 53.59: 225 53.59 - 71.45: 88 71.45 - 89.31: 23 Dihedral angle restraints: 10467 sinusoidal: 4701 harmonic: 5766 Sorted by residual: dihedral pdb=" CA THR A 192 " pdb=" C THR A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA THR B 192 " pdb=" C THR B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR C 192 " pdb=" C THR C 192 " pdb=" N TYR C 193 " pdb=" CA TYR C 193 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 10464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1762 0.027 - 0.053: 576 0.053 - 0.080: 235 0.080 - 0.107: 142 0.107 - 0.133: 99 Chirality restraints: 2814 Sorted by residual: chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE F 79 " pdb=" N ILE F 79 " pdb=" C ILE F 79 " pdb=" CB ILE F 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE E 79 " pdb=" N ILE E 79 " pdb=" C ILE E 79 " pdb=" CB ILE E 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2811 not shown) Planarity restraints: 2848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A 262 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 49 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO B 50 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U H 26 " -0.014 2.00e-02 2.50e+03 7.95e-03 1.42e+00 pdb=" N1 U H 26 " 0.019 2.00e-02 2.50e+03 pdb=" C2 U H 26 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U H 26 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U H 26 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U H 26 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U H 26 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U H 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U H 26 " 0.001 2.00e-02 2.50e+03 ... (remaining 2845 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1074 2.74 - 3.28: 15256 3.28 - 3.82: 27985 3.82 - 4.36: 34297 4.36 - 4.90: 57911 Nonbonded interactions: 136523 Sorted by model distance: nonbonded pdb=" OG1 THR D 321 " pdb=" OE2 GLU D 326 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR B 193 " pdb=" OE1 GLU B 304 " model vdw 2.346 3.040 nonbonded pdb=" O LYS F 226 " pdb=" NZ LYS F 226 " model vdw 2.362 3.120 nonbonded pdb=" NZ LYS F 70 " pdb=" OG1 THR F 195 " model vdw 2.367 3.120 ... (remaining 136518 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' and (resid 1 through 20 or resid 22 through 344)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 20 or resid 22 through 344)) selection = (chain 'E' and (resid 1 through 20 or resid 22 through 344)) selection = (chain 'F' and (resid 1 through 20 or resid 22 through 344)) } 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: 6.280 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.870 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.002 0.026 17448 Z= 0.089 Angle : 0.407 7.867 23958 Z= 0.242 Chirality : 0.041 0.133 2814 Planarity : 0.003 0.041 2848 Dihedral : 15.711 89.314 6743 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.02 % Allowed : 16.28 % Favored : 82.70 % 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: 0.52 (0.19), residues: 1971 helix: 1.38 (0.24), residues: 509 sheet: 1.44 (0.30), residues: 328 loop : -0.47 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 138 TYR 0.007 0.001 TYR C 225 PHE 0.010 0.001 PHE F 7 TRP 0.003 0.001 TRP E 332 HIS 0.003 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.09 (17448) covalent geometry : angle 0.40743 / 0.24 (23958) hydrogen bonds : bond 0.14172 / 9.50 ( 643) hydrogen bonds : angle 6.35742 / 4.56 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.616 Fit side-chains REVERT: A 16 ASP cc_start: 0.8618 (t0) cc_final: 0.8059 (t0) REVERT: A 18 GLN cc_start: 0.8650 (mt0) cc_final: 0.8162 (mp10) REVERT: A 199 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7824 (p0) REVERT: A 215 GLU cc_start: 0.7608 (tt0) cc_final: 0.7017 (tp30) REVERT: A 232 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: A 330 MET cc_start: 0.8416 (tpp) cc_final: 0.7709 (tpt) REVERT: B 64 LYS cc_start: 0.8096 (mptt) cc_final: 0.7775 (mptp) REVERT: B 204 LYS cc_start: 0.8087 (mttp) cc_final: 0.7301 (mmpt) REVERT: B 258 PHE cc_start: 0.7806 (t80) cc_final: 0.7434 (t80) REVERT: C 149 LYS cc_start: 0.7919 (mttt) cc_final: 0.7511 (mppt) REVERT: C 152 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8017 (mm110) REVERT: D 103 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7568 (m) REVERT: D 152 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7506 (mt0) REVERT: E 202 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6774 (mt-10) REVERT: E 251 LEU cc_start: 0.7729 (tp) cc_final: 0.7519 (tp) REVERT: E 263 PHE cc_start: 0.7746 (p90) cc_final: 0.7531 (p90) REVERT: E 284 GLN cc_start: 0.7096 (tt0) cc_final: 0.6214 (tp40) REVERT: E 330 MET cc_start: 0.6063 (tpp) cc_final: 0.5801 (ttt) REVERT: F 138 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7468 (mtp85) REVERT: F 144 THR cc_start: 0.8778 (m) cc_final: 0.8376 (p) REVERT: F 188 GLN cc_start: 0.7906 (tt0) cc_final: 0.7476 (tp-100) REVERT: F 191 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7179 (mp0) outliers start: 18 outliers final: 11 residues processed: 161 average time/residue: 0.6479 time to fit residues: 116.0915 Evaluate side-chains 153 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129614 restraints weight = 17054.144| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.97 r_work: 0.3042 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17448 Z= 0.115 Angle : 0.456 7.239 23958 Z= 0.251 Chirality : 0.043 0.143 2814 Planarity : 0.004 0.041 2848 Dihedral : 10.786 73.535 3016 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.18 % Allowed : 14.29 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1971 helix: 1.25 (0.24), residues: 509 sheet: 1.35 (0.29), residues: 335 loop : -0.49 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.009 0.001 TYR F 342 PHE 0.014 0.001 PHE F 268 TRP 0.009 0.001 TRP E 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (17448) covalent geometry : angle 0.45625 / 0.25 (23958) hydrogen bonds : bond 0.04216 / 2.78 ( 643) hydrogen bonds : angle 5.30889 / 3.76 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.637 Fit side-chains REVERT: A 18 GLN cc_start: 0.8849 (mt0) cc_final: 0.8365 (mp10) REVERT: A 36 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6709 (t0) REVERT: A 199 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8163 (p0) REVERT: A 200 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 204 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8427 (mptp) REVERT: A 215 GLU cc_start: 0.7965 (tt0) cc_final: 0.7288 (tp30) REVERT: A 232 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: A 330 MET cc_start: 0.8673 (tpp) cc_final: 0.7905 (tpt) REVERT: B 64 LYS cc_start: 0.8174 (mptt) cc_final: 0.7800 (mptp) REVERT: B 204 LYS cc_start: 0.8051 (mttp) cc_final: 0.7231 (mmpt) REVERT: B 258 PHE cc_start: 0.7661 (t80) cc_final: 0.7314 (t80) REVERT: B 317 VAL cc_start: 0.7755 (t) cc_final: 0.7533 (p) REVERT: C 149 LYS cc_start: 0.8077 (mttt) cc_final: 0.7546 (mppt) REVERT: C 152 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8213 (mm110) REVERT: C 264 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: D 68 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: D 103 SER cc_start: 0.7995 (p) cc_final: 0.7593 (m) REVERT: D 152 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7523 (mt0) REVERT: D 173 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8047 (tttt) REVERT: E 136 ASN cc_start: 0.8094 (m-40) cc_final: 0.7875 (m110) REVERT: E 202 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6821 (mt-10) REVERT: E 251 LEU cc_start: 0.7699 (tp) cc_final: 0.7464 (tp) REVERT: E 263 PHE cc_start: 0.7739 (p90) cc_final: 0.7475 (p90) REVERT: E 284 GLN cc_start: 0.6986 (tt0) cc_final: 0.6158 (tp40) REVERT: E 330 MET cc_start: 0.5684 (tpp) cc_final: 0.5413 (ttt) REVERT: F 21 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: F 68 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: F 138 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7519 (mtp85) REVERT: F 144 THR cc_start: 0.8825 (m) cc_final: 0.8395 (p) REVERT: F 188 GLN cc_start: 0.8046 (tt0) cc_final: 0.7537 (tp-100) REVERT: F 191 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7200 (mp0) outliers start: 56 outliers final: 20 residues processed: 187 average time/residue: 0.6066 time to fit residues: 127.0531 Evaluate side-chains 171 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 108 optimal weight: 0.0370 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.178126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130183 restraints weight = 17151.351| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.02 r_work: 0.3053 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17448 Z= 0.102 Angle : 0.437 6.728 23958 Z= 0.240 Chirality : 0.043 0.142 2814 Planarity : 0.003 0.039 2848 Dihedral : 10.740 73.384 3003 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.95 % Allowed : 14.58 % Favored : 82.47 % 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: 0.44 (0.18), residues: 1971 helix: 1.22 (0.24), residues: 509 sheet: 1.50 (0.29), residues: 328 loop : -0.51 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 257 TYR 0.009 0.001 TYR A 342 PHE 0.013 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (17448) covalent geometry : angle 0.43723 / 0.24 (23958) hydrogen bonds : bond 0.03830 / 2.54 ( 643) hydrogen bonds : angle 5.04887 / 3.56 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.703 Fit side-chains REVERT: A 18 GLN cc_start: 0.8858 (mt0) cc_final: 0.8393 (mp10) REVERT: A 200 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 204 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8420 (mptp) REVERT: A 215 GLU cc_start: 0.7996 (tt0) cc_final: 0.7330 (tp30) REVERT: A 232 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: B 64 LYS cc_start: 0.8209 (mptt) cc_final: 0.7907 (mptp) REVERT: B 204 LYS cc_start: 0.8063 (mttp) cc_final: 0.7253 (mmpt) REVERT: B 258 PHE cc_start: 0.7667 (t80) cc_final: 0.7322 (t80) REVERT: B 317 VAL cc_start: 0.7800 (t) cc_final: 0.7579 (p) REVERT: C 149 LYS cc_start: 0.8080 (mttt) cc_final: 0.7554 (mppt) REVERT: C 152 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8203 (mm110) REVERT: C 264 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: D 68 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: D 103 SER cc_start: 0.7952 (p) cc_final: 0.7554 (m) REVERT: D 152 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7501 (mt0) REVERT: D 173 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7956 (tttt) REVERT: E 136 ASN cc_start: 0.8186 (m-40) cc_final: 0.7957 (m110) REVERT: E 202 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6851 (mt-10) REVERT: E 251 LEU cc_start: 0.7736 (tp) cc_final: 0.7484 (tp) REVERT: E 263 PHE cc_start: 0.7779 (p90) cc_final: 0.7552 (p90) REVERT: E 284 GLN cc_start: 0.7100 (tt0) cc_final: 0.6222 (tp40) REVERT: E 330 MET cc_start: 0.5816 (tpp) cc_final: 0.5577 (ttt) REVERT: F 21 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: F 68 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: F 138 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7404 (mtp85) REVERT: F 144 THR cc_start: 0.8810 (m) cc_final: 0.8361 (p) REVERT: F 183 ASP cc_start: 0.7497 (m-30) cc_final: 0.7123 (m-30) REVERT: F 188 GLN cc_start: 0.8008 (tt0) cc_final: 0.7497 (tp-100) REVERT: F 191 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7194 (mp0) REVERT: F 232 PHE cc_start: 0.5981 (OUTLIER) cc_final: 0.5589 (t80) REVERT: F 264 GLU cc_start: 0.6496 (mm-30) cc_final: 0.5535 (tt0) outliers start: 52 outliers final: 21 residues processed: 190 average time/residue: 0.5941 time to fit residues: 126.8193 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 51 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128701 restraints weight = 17151.976| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.90 r_work: 0.3073 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17448 Z= 0.096 Angle : 0.429 6.577 23958 Z= 0.236 Chirality : 0.043 0.141 2814 Planarity : 0.003 0.039 2848 Dihedral : 10.660 73.401 2998 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.84 % Allowed : 15.26 % Favored : 81.91 % 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: 0.48 (0.18), residues: 1971 helix: 1.25 (0.24), residues: 509 sheet: 1.60 (0.29), residues: 326 loop : -0.50 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 257 TYR 0.008 0.001 TYR A 342 PHE 0.012 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (17448) covalent geometry : angle 0.42864 / 0.24 (23958) hydrogen bonds : bond 0.03541 / 2.35 ( 643) hydrogen bonds : angle 4.92816 / 3.47 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.762 Fit side-chains REVERT: A 18 GLN cc_start: 0.8856 (mt0) cc_final: 0.8410 (mp10) REVERT: A 188 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: A 199 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 200 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 204 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8386 (mptp) REVERT: A 215 GLU cc_start: 0.8016 (tt0) cc_final: 0.7365 (tp30) REVERT: A 232 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: B 200 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7098 (tp) REVERT: B 204 LYS cc_start: 0.8073 (mttp) cc_final: 0.7270 (mmpt) REVERT: B 258 PHE cc_start: 0.7761 (t80) cc_final: 0.7410 (t80) REVERT: B 317 VAL cc_start: 0.7892 (t) cc_final: 0.7686 (p) REVERT: C 149 LYS cc_start: 0.8065 (mttt) cc_final: 0.7557 (mppt) REVERT: C 152 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8207 (mm110) REVERT: C 264 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: D 68 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: D 103 SER cc_start: 0.7938 (p) cc_final: 0.7530 (m) REVERT: D 152 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7525 (mt0) REVERT: D 173 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7986 (tttt) REVERT: E 136 ASN cc_start: 0.8208 (m-40) cc_final: 0.7986 (m110) REVERT: E 202 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6911 (mt-10) REVERT: E 251 LEU cc_start: 0.7820 (tp) cc_final: 0.7556 (tp) REVERT: E 263 PHE cc_start: 0.7789 (p90) cc_final: 0.7550 (p90) REVERT: E 284 GLN cc_start: 0.7155 (tt0) cc_final: 0.6288 (tp40) REVERT: E 330 MET cc_start: 0.5909 (tpp) cc_final: 0.5685 (ttt) REVERT: F 21 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: F 68 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: F 138 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7420 (mtp85) REVERT: F 144 THR cc_start: 0.8820 (m) cc_final: 0.8389 (p) REVERT: F 188 GLN cc_start: 0.8005 (tt0) cc_final: 0.7526 (tp-100) REVERT: F 191 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7256 (mp0) REVERT: F 232 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5535 (t80) REVERT: F 264 GLU cc_start: 0.6513 (mm-30) cc_final: 0.5597 (tt0) outliers start: 50 outliers final: 21 residues processed: 178 average time/residue: 0.6005 time to fit residues: 119.8999 Evaluate side-chains 172 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 169 optimal weight: 4.9990 chunk 109 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 174 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 overall best weight: 1.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129244 restraints weight = 16945.311| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.76 r_work: 0.3060 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17448 Z= 0.123 Angle : 0.459 5.963 23958 Z= 0.251 Chirality : 0.044 0.150 2814 Planarity : 0.004 0.042 2848 Dihedral : 10.699 73.443 2996 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.35 % Allowed : 14.52 % Favored : 82.13 % 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: 0.38 (0.18), residues: 1971 helix: 1.18 (0.24), residues: 506 sheet: 1.56 (0.29), residues: 329 loop : -0.58 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.011 0.001 TYR A 342 PHE 0.014 0.001 PHE F 268 TRP 0.011 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (17448) covalent geometry : angle 0.45865 / 0.25 (23958) hydrogen bonds : bond 0.03879 / 2.55 ( 643) hydrogen bonds : angle 4.98528 / 3.51 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 0.594 Fit side-chains REVERT: A 18 GLN cc_start: 0.8833 (mt0) cc_final: 0.8393 (mp10) REVERT: A 21 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: A 188 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: A 199 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8215 (p0) REVERT: A 200 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8227 (mp) REVERT: A 204 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8364 (mptp) REVERT: A 215 GLU cc_start: 0.7948 (tt0) cc_final: 0.7289 (tp30) REVERT: A 232 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: B 200 LEU cc_start: 0.7417 (mt) cc_final: 0.7203 (tp) REVERT: B 204 LYS cc_start: 0.8071 (mttp) cc_final: 0.7254 (mmpt) REVERT: B 258 PHE cc_start: 0.7695 (t80) cc_final: 0.7335 (t80) REVERT: B 301 ASP cc_start: 0.7198 (m-30) cc_final: 0.6922 (m-30) REVERT: B 317 VAL cc_start: 0.7834 (t) cc_final: 0.7617 (p) REVERT: C 149 LYS cc_start: 0.8114 (mttt) cc_final: 0.7585 (mppt) REVERT: C 152 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8183 (mm110) REVERT: C 188 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: C 264 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: D 68 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: D 103 SER cc_start: 0.7950 (p) cc_final: 0.7555 (m) REVERT: D 152 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7484 (mt0) REVERT: D 173 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8084 (tttt) REVERT: E 136 ASN cc_start: 0.8156 (m-40) cc_final: 0.7934 (m110) REVERT: E 251 LEU cc_start: 0.7804 (tp) cc_final: 0.7518 (tp) REVERT: E 263 PHE cc_start: 0.7776 (p90) cc_final: 0.7571 (p90) REVERT: E 284 GLN cc_start: 0.7138 (tt0) cc_final: 0.6254 (tp40) REVERT: E 330 MET cc_start: 0.5770 (tpp) cc_final: 0.5511 (ttt) REVERT: F 21 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: F 68 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: F 138 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7355 (mtp85) REVERT: F 144 THR cc_start: 0.8802 (m) cc_final: 0.8343 (p) REVERT: F 188 GLN cc_start: 0.8021 (tt0) cc_final: 0.7559 (tp-100) REVERT: F 191 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7205 (mp0) REVERT: F 264 GLU cc_start: 0.6493 (mm-30) cc_final: 0.5555 (tt0) outliers start: 59 outliers final: 29 residues processed: 185 average time/residue: 0.5911 time to fit residues: 122.7813 Evaluate side-chains 174 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127346 restraints weight = 16886.985| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.75 r_work: 0.3028 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17448 Z= 0.176 Angle : 0.528 6.364 23958 Z= 0.287 Chirality : 0.046 0.172 2814 Planarity : 0.004 0.060 2848 Dihedral : 10.855 73.483 2996 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.29 % Allowed : 15.20 % Favored : 81.51 % 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: 0.11 (0.18), residues: 1971 helix: 0.92 (0.23), residues: 506 sheet: 1.47 (0.29), residues: 327 loop : -0.75 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 90 TYR 0.015 0.001 TYR A 342 PHE 0.018 0.002 PHE F 268 TRP 0.013 0.002 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (17448) covalent geometry : angle 0.52816 / 0.29 (23958) hydrogen bonds : bond 0.04598 / 3.00 ( 643) hydrogen bonds : angle 5.19855 / 3.65 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.688 Fit side-chains REVERT: A 18 GLN cc_start: 0.8941 (mt0) cc_final: 0.8475 (mp10) REVERT: A 21 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8197 (mm-30) REVERT: A 199 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8261 (p0) REVERT: A 200 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 204 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8451 (mptp) REVERT: A 215 GLU cc_start: 0.8008 (tt0) cc_final: 0.7355 (tp30) REVERT: A 232 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: B 68 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 191 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: B 200 LEU cc_start: 0.7526 (mt) cc_final: 0.7318 (tp) REVERT: B 204 LYS cc_start: 0.8090 (mttp) cc_final: 0.7273 (mmpt) REVERT: B 258 PHE cc_start: 0.7724 (t80) cc_final: 0.7391 (t80) REVERT: B 317 VAL cc_start: 0.7850 (t) cc_final: 0.7646 (p) REVERT: C 149 LYS cc_start: 0.8198 (mttt) cc_final: 0.7634 (mppt) REVERT: C 152 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8205 (mm110) REVERT: C 188 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8011 (tp40) REVERT: C 264 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7082 (mm-30) REVERT: D 152 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7512 (mt0) REVERT: D 173 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8103 (tttt) REVERT: E 46 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8581 (mptp) REVERT: E 251 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7607 (tp) REVERT: E 263 PHE cc_start: 0.7871 (p90) cc_final: 0.7633 (p90) REVERT: E 284 GLN cc_start: 0.7216 (tt0) cc_final: 0.6272 (tp40) REVERT: E 330 MET cc_start: 0.5773 (tpp) cc_final: 0.5534 (ttt) REVERT: F 21 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: F 138 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7452 (mtp85) REVERT: F 144 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8387 (p) REVERT: F 188 GLN cc_start: 0.8058 (tt0) cc_final: 0.7598 (tp-100) REVERT: F 191 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7314 (mp0) REVERT: F 245 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6950 (tt) REVERT: F 264 GLU cc_start: 0.6531 (mm-30) cc_final: 0.5584 (tt0) outliers start: 58 outliers final: 27 residues processed: 175 average time/residue: 0.6016 time to fit residues: 118.2595 Evaluate side-chains 164 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 44 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128967 restraints weight = 16906.936| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.96 r_work: 0.3027 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17448 Z= 0.134 Angle : 0.475 5.738 23958 Z= 0.261 Chirality : 0.044 0.146 2814 Planarity : 0.004 0.044 2848 Dihedral : 10.806 73.484 2996 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.84 % Allowed : 15.71 % Favored : 81.45 % 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: 0.12 (0.18), residues: 1971 helix: 0.98 (0.24), residues: 506 sheet: 1.35 (0.29), residues: 333 loop : -0.74 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.013 0.001 TYR A 342 PHE 0.014 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (17448) covalent geometry : angle 0.47542 / 0.26 (23958) hydrogen bonds : bond 0.04078 / 2.68 ( 643) hydrogen bonds : angle 5.07413 / 3.57 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.670 Fit side-chains REVERT: A 18 GLN cc_start: 0.8925 (mt0) cc_final: 0.8441 (mp10) REVERT: A 21 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: A 188 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: A 199 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8277 (p0) REVERT: A 200 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 204 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8413 (mptp) REVERT: A 215 GLU cc_start: 0.7982 (tt0) cc_final: 0.7316 (tp30) REVERT: A 232 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: B 68 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: B 200 LEU cc_start: 0.7518 (mt) cc_final: 0.7312 (tp) REVERT: B 204 LYS cc_start: 0.8069 (mttp) cc_final: 0.7248 (mmpt) REVERT: B 258 PHE cc_start: 0.7701 (t80) cc_final: 0.7412 (t80) REVERT: B 317 VAL cc_start: 0.7836 (t) cc_final: 0.7615 (p) REVERT: C 149 LYS cc_start: 0.8157 (mttt) cc_final: 0.7584 (mppt) REVERT: C 152 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8225 (mm110) REVERT: C 188 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7989 (tp-100) REVERT: C 264 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: D 152 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7509 (mt0) REVERT: D 173 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8051 (tttt) REVERT: D 264 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6371 (tt0) REVERT: E 251 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7546 (tp) REVERT: E 263 PHE cc_start: 0.7867 (p90) cc_final: 0.7622 (p90) REVERT: E 284 GLN cc_start: 0.7193 (tt0) cc_final: 0.6301 (tp40) REVERT: E 330 MET cc_start: 0.5793 (tpp) cc_final: 0.5561 (ttt) REVERT: F 21 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: F 68 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: F 138 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7446 (mtp85) REVERT: F 144 THR cc_start: 0.8830 (m) cc_final: 0.8359 (p) REVERT: F 191 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7341 (mp0) REVERT: F 245 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6906 (tt) REVERT: F 264 GLU cc_start: 0.6508 (mm-30) cc_final: 0.5570 (tt0) outliers start: 50 outliers final: 24 residues processed: 172 average time/residue: 0.6122 time to fit residues: 117.9244 Evaluate side-chains 166 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126634 restraints weight = 17109.188| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.70 r_work: 0.3036 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17448 Z= 0.120 Angle : 0.463 5.869 23958 Z= 0.254 Chirality : 0.044 0.147 2814 Planarity : 0.004 0.042 2848 Dihedral : 10.774 73.480 2996 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.61 % Allowed : 16.11 % 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 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: 0.17 (0.18), residues: 1971 helix: 1.04 (0.24), residues: 506 sheet: 1.35 (0.29), residues: 333 loop : -0.71 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.011 0.001 TYR A 342 PHE 0.013 0.001 PHE F 268 TRP 0.009 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (17448) covalent geometry : angle 0.46255 / 0.25 (23958) hydrogen bonds : bond 0.03886 / 2.56 ( 643) hydrogen bonds : angle 5.01146 / 3.53 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.669 Fit side-chains REVERT: A 18 GLN cc_start: 0.8896 (mt0) cc_final: 0.8408 (mp10) REVERT: A 21 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: A 188 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: A 199 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8313 (p0) REVERT: A 200 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 204 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8421 (mptp) REVERT: A 215 GLU cc_start: 0.7978 (tt0) cc_final: 0.7307 (tp30) REVERT: A 232 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: B 68 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: B 191 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: B 200 LEU cc_start: 0.7490 (mt) cc_final: 0.7281 (tp) REVERT: B 204 LYS cc_start: 0.8053 (mttp) cc_final: 0.7230 (mmpt) REVERT: B 258 PHE cc_start: 0.7643 (t80) cc_final: 0.7348 (t80) REVERT: B 317 VAL cc_start: 0.7801 (t) cc_final: 0.7582 (p) REVERT: C 149 LYS cc_start: 0.8152 (mttt) cc_final: 0.7572 (mppt) REVERT: C 152 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8214 (mm110) REVERT: C 188 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7987 (tp-100) REVERT: C 264 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: D 152 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7481 (mt0) REVERT: D 173 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: D 264 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6341 (tt0) REVERT: E 251 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7491 (tp) REVERT: E 263 PHE cc_start: 0.7832 (p90) cc_final: 0.7575 (p90) REVERT: E 284 GLN cc_start: 0.7156 (tt0) cc_final: 0.6258 (tp40) REVERT: E 330 MET cc_start: 0.5677 (tpp) cc_final: 0.5448 (ttt) REVERT: F 21 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: F 68 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: F 138 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7412 (mtp85) REVERT: F 144 THR cc_start: 0.8809 (m) cc_final: 0.8337 (p) REVERT: F 191 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7303 (mp0) REVERT: F 245 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6876 (tt) REVERT: F 264 GLU cc_start: 0.6472 (mm-30) cc_final: 0.5507 (tt0) outliers start: 46 outliers final: 22 residues processed: 164 average time/residue: 0.6038 time to fit residues: 110.8312 Evaluate side-chains 164 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127681 restraints weight = 16936.490| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.77 r_work: 0.3026 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17448 Z= 0.162 Angle : 0.509 5.955 23958 Z= 0.277 Chirality : 0.046 0.155 2814 Planarity : 0.004 0.057 2848 Dihedral : 10.843 73.507 2996 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.95 % Allowed : 15.77 % 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 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: 0.04 (0.18), residues: 1971 helix: 0.88 (0.23), residues: 506 sheet: 1.39 (0.29), residues: 327 loop : -0.81 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.014 0.001 TYR B 193 PHE 0.016 0.002 PHE F 268 TRP 0.011 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (17448) covalent geometry : angle 0.50946 / 0.28 (23958) hydrogen bonds : bond 0.04380 / 2.87 ( 643) hydrogen bonds : angle 5.13787 / 3.61 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.674 Fit side-chains REVERT: A 18 GLN cc_start: 0.8916 (mt0) cc_final: 0.8438 (mp10) REVERT: A 21 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: A 199 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (p0) REVERT: A 200 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 204 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8443 (mptp) REVERT: A 215 GLU cc_start: 0.7987 (tt0) cc_final: 0.7311 (tp30) REVERT: A 232 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: B 68 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 191 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: B 200 LEU cc_start: 0.7557 (mt) cc_final: 0.7352 (tp) REVERT: B 204 LYS cc_start: 0.8074 (mttp) cc_final: 0.7256 (mmpt) REVERT: B 258 PHE cc_start: 0.7690 (t80) cc_final: 0.7390 (t80) REVERT: B 317 VAL cc_start: 0.7827 (t) cc_final: 0.7611 (p) REVERT: C 149 LYS cc_start: 0.8191 (mttt) cc_final: 0.7628 (mppt) REVERT: C 152 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8198 (mm110) REVERT: C 188 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8013 (tp-100) REVERT: C 264 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7027 (mm-30) REVERT: D 68 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: D 152 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7507 (mt0) REVERT: D 173 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8066 (tttt) REVERT: D 264 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6380 (tt0) REVERT: E 251 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7565 (tp) REVERT: E 263 PHE cc_start: 0.7846 (p90) cc_final: 0.7597 (p90) REVERT: E 284 GLN cc_start: 0.7208 (tt0) cc_final: 0.6311 (tp40) REVERT: E 330 MET cc_start: 0.5682 (tpp) cc_final: 0.5413 (ttt) REVERT: F 21 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: F 68 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: F 138 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7422 (mtp85) REVERT: F 144 THR cc_start: 0.8827 (m) cc_final: 0.8350 (p) REVERT: F 191 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7350 (mp0) REVERT: F 245 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6865 (tt) REVERT: F 264 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5561 (tt0) outliers start: 52 outliers final: 28 residues processed: 169 average time/residue: 0.6467 time to fit residues: 121.7700 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 0.0070 chunk 108 optimal weight: 6.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124485 restraints weight = 16897.262| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.66 r_work: 0.3025 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 17448 Z= 0.151 Angle : 0.723 61.570 23958 Z= 0.359 Chirality : 0.045 0.155 2814 Planarity : 0.004 0.055 2848 Dihedral : 10.841 73.517 2996 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.61 % Allowed : 16.00 % Favored : 81.40 % Cbeta Deviations : 0.05 % 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: 0.04 (0.18), residues: 1971 helix: 0.89 (0.23), residues: 506 sheet: 1.39 (0.29), residues: 327 loop : -0.81 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 138 TYR 0.013 0.001 TYR A 342 PHE 0.016 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17448) covalent geometry : angle 0.72267 / 0.36 (23958) hydrogen bonds : bond 0.04308 / 2.82 ( 643) hydrogen bonds : angle 5.13093 / 3.61 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.816 Fit side-chains REVERT: A 18 GLN cc_start: 0.8920 (mt0) cc_final: 0.8440 (mp10) REVERT: A 21 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: A 199 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8288 (p0) REVERT: A 200 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 204 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8443 (mptp) REVERT: A 215 GLU cc_start: 0.7995 (tt0) cc_final: 0.7314 (tp30) REVERT: A 232 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: B 68 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 191 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: B 204 LYS cc_start: 0.8065 (mttp) cc_final: 0.7244 (mmpt) REVERT: B 258 PHE cc_start: 0.7673 (t80) cc_final: 0.7371 (t80) REVERT: B 317 VAL cc_start: 0.7818 (t) cc_final: 0.7601 (p) REVERT: C 149 LYS cc_start: 0.8191 (mttt) cc_final: 0.7626 (mppt) REVERT: C 152 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8204 (mm110) REVERT: C 188 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8013 (tp-100) REVERT: C 264 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: D 68 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: D 152 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7498 (mt0) REVERT: D 173 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8062 (tttt) REVERT: D 264 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6358 (tt0) REVERT: E 251 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7554 (tp) REVERT: E 263 PHE cc_start: 0.7834 (p90) cc_final: 0.7581 (p90) REVERT: E 284 GLN cc_start: 0.7178 (tt0) cc_final: 0.6294 (tp40) REVERT: E 330 MET cc_start: 0.5658 (tpp) cc_final: 0.5392 (ttt) REVERT: F 21 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: F 68 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: F 138 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7424 (mtp85) REVERT: F 144 THR cc_start: 0.8838 (m) cc_final: 0.8363 (p) REVERT: F 191 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7339 (mp0) REVERT: F 245 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6838 (tt) REVERT: F 264 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5541 (tt0) outliers start: 46 outliers final: 27 residues processed: 162 average time/residue: 0.6381 time to fit residues: 115.4281 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.0770 chunk 194 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127225 restraints weight = 16856.431| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.76 r_work: 0.3034 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 17448 Z= 0.151 Angle : 0.723 61.569 23958 Z= 0.359 Chirality : 0.045 0.155 2814 Planarity : 0.004 0.055 2848 Dihedral : 10.841 73.517 2996 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.38 % Allowed : 16.22 % Favored : 81.40 % Cbeta Deviations : 0.05 % 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: 0.04 (0.18), residues: 1971 helix: 0.89 (0.23), residues: 506 sheet: 1.39 (0.29), residues: 327 loop : -0.81 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 138 TYR 0.013 0.001 TYR A 342 PHE 0.016 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17448) covalent geometry : angle 0.72266 / 0.36 (23958) hydrogen bonds : bond 0.04308 / 2.82 ( 643) hydrogen bonds : angle 5.13093 / 3.61 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7085.87 seconds wall clock time: 121 minutes 30.62 seconds (7290.62 seconds total)