Starting phenix.real_space_refine on Wed Mar 4 23:54:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m48_63618/03_2026/9m48_63618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m48_63618/03_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_63618/03_2026/9m48_63618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m48_63618/03_2026/9m48_63618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m48_63618/03_2026/9m48_63618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m48_63618/03_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-5986/lib/python3.9/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, 1 Unusual residues: {' CO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.26 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: 1.42 Conformation dependent library (CDL) restraints added in 752.2 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: 2.29 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: 3.36 Time building geometry restraints manager: 1.94 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=" 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 angle pdb=" C LEU A 245 " pdb=" N GLY A 246 " pdb=" CA GLY A 246 " ideal model delta sigma weight residual 122.73 121.02 1.71 9.30e-01 1.16e+00 3.37e+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: 4.400 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.390 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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= 0.083 Angle : 0.407 7.867 23958 Z= 0.225 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 covalent geometry : bond 0.00168 (17448) covalent geometry : angle 0.40741 (23958) hydrogen bonds : bond 0.14172 ( 643) hydrogen bonds : angle 6.35742 ( 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 : 0.726 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: 0.6880 time to fit residues: 122.7464 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 : 0.748 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN E 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131872 restraints weight = 17085.351| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.58 r_work: 0.3022 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17448 Z= 0.114 Angle : 0.458 7.070 23958 Z= 0.250 Chirality : 0.043 0.144 2814 Planarity : 0.004 0.039 2848 Dihedral : 10.750 73.425 3016 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.12 % Allowed : 14.18 % 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: 0.41 (0.18), residues: 1971 helix: 1.20 (0.24), residues: 509 sheet: 1.43 (0.29), residues: 327 loop : -0.50 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 90 TYR 0.009 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 covalent geometry : bond 0.00267 (17448) covalent geometry : angle 0.45768 (23958) hydrogen bonds : bond 0.03943 ( 643) hydrogen bonds : angle 5.17145 ( 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 201 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 0.570 Fit side-chains REVERT: A 18 GLN cc_start: 0.8796 (mt0) cc_final: 0.8436 (mp10) REVERT: A 200 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 204 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8438 (mptp) REVERT: A 215 GLU cc_start: 0.7921 (tt0) cc_final: 0.7402 (tp30) REVERT: A 232 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: A 330 MET cc_start: 0.8675 (tpp) cc_final: 0.7838 (tpt) REVERT: B 204 LYS cc_start: 0.8114 (mttp) cc_final: 0.7345 (mmpt) REVERT: B 258 PHE cc_start: 0.7825 (t80) cc_final: 0.7474 (t80) REVERT: C 149 LYS cc_start: 0.8079 (mttt) cc_final: 0.7646 (mppt) REVERT: C 264 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: D 68 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: D 103 SER cc_start: 0.7987 (p) cc_final: 0.7601 (m) REVERT: D 173 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7999 (tttt) REVERT: E 202 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6834 (mt-10) REVERT: E 251 LEU cc_start: 0.7805 (tp) cc_final: 0.7567 (tp) REVERT: E 263 PHE cc_start: 0.7794 (p90) cc_final: 0.7591 (p90) REVERT: E 284 GLN cc_start: 0.7194 (tt0) cc_final: 0.6343 (tp40) REVERT: E 330 MET cc_start: 0.5894 (tpp) cc_final: 0.5619 (ttt) REVERT: F 21 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: F 68 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: F 138 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7566 (mtp85) REVERT: F 144 THR cc_start: 0.8818 (m) cc_final: 0.8445 (p) REVERT: F 183 ASP cc_start: 0.7333 (m-30) cc_final: 0.7091 (m-30) REVERT: F 188 GLN cc_start: 0.7994 (tt0) cc_final: 0.7596 (tp-100) REVERT: F 191 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7277 (mp0) REVERT: F 232 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5616 (t80) REVERT: F 264 GLU cc_start: 0.6493 (mm-30) cc_final: 0.5675 (tt0) outliers start: 55 outliers final: 21 residues processed: 193 average time/residue: 0.6096 time to fit residues: 131.7131 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 : 0.659 ------------------------------------------------------------------------------- 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 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 B residue 303 VAL 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 149 LYS 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 108 optimal weight: 0.0020 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132246 restraints weight = 17216.323| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.89 r_work: 0.3048 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0808 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= 0.095 Angle : 0.430 6.666 23958 Z= 0.235 Chirality : 0.043 0.143 2814 Planarity : 0.003 0.038 2848 Dihedral : 10.628 73.442 2998 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: 0.46 (0.18), residues: 1971 helix: 1.22 (0.24), residues: 509 sheet: 1.58 (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 D 138 TYR 0.008 0.001 TYR A 342 PHE 0.011 0.001 PHE F 268 TRP 0.013 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00218 (17448) covalent geometry : angle 0.43048 (23958) hydrogen bonds : bond 0.03456 ( 643) hydrogen bonds : angle 4.88419 ( 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 204 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.665 Fit side-chains REVERT: A 18 GLN cc_start: 0.8917 (mt0) cc_final: 0.8471 (mp10) REVERT: A 188 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: A 199 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (p0) REVERT: A 200 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 204 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8412 (mptp) REVERT: A 215 GLU cc_start: 0.8045 (tt0) cc_final: 0.7401 (tp30) REVERT: A 232 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: B 64 LYS cc_start: 0.8230 (mptt) cc_final: 0.7869 (mptp) REVERT: B 200 LEU cc_start: 0.7456 (mt) cc_final: 0.7211 (tp) REVERT: B 204 LYS cc_start: 0.8093 (mttp) cc_final: 0.7299 (mmpt) REVERT: B 258 PHE cc_start: 0.7783 (t80) cc_final: 0.7444 (t80) REVERT: C 149 LYS cc_start: 0.8112 (mttt) cc_final: 0.7611 (mppt) REVERT: C 264 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: D 68 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: D 103 SER cc_start: 0.7960 (p) cc_final: 0.7600 (m) REVERT: D 173 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7968 (tttt) REVERT: E 166 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8648 (m) REVERT: E 202 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6902 (mt-10) REVERT: E 251 LEU cc_start: 0.7875 (tp) cc_final: 0.7599 (tp) REVERT: E 263 PHE cc_start: 0.7795 (p90) cc_final: 0.7528 (p90) REVERT: E 284 GLN cc_start: 0.7205 (tt0) cc_final: 0.6279 (tp40) REVERT: E 330 MET cc_start: 0.5887 (tpp) cc_final: 0.5623 (ttt) REVERT: F 21 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: F 68 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: F 138 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7444 (mtp85) REVERT: F 144 THR cc_start: 0.8822 (m) cc_final: 0.8407 (p) REVERT: F 188 GLN cc_start: 0.8037 (tt0) cc_final: 0.7534 (tp-100) REVERT: F 191 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7246 (mp0) REVERT: F 264 GLU cc_start: 0.6556 (mm-30) cc_final: 0.5613 (tt0) outliers start: 56 outliers final: 17 residues processed: 193 average time/residue: 0.6013 time to fit residues: 130.3374 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 96 ILE 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 Chi-restraints excluded: chain F residue 325 THR 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: 1.9990 chunk 156 optimal weight: 0.0030 chunk 25 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN E 136 ASN F 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134157 restraints weight = 17179.537| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.59 r_work: 0.3049 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17448 Z= 0.079 Angle : 0.411 6.096 23958 Z= 0.224 Chirality : 0.042 0.139 2814 Planarity : 0.003 0.035 2848 Dihedral : 10.570 73.458 2996 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.44 % Allowed : 15.09 % 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: 0.55 (0.18), residues: 1971 helix: 1.33 (0.24), residues: 509 sheet: 1.76 (0.29), residues: 317 loop : -0.49 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.007 0.001 TYR C 225 PHE 0.010 0.001 PHE E 7 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00173 (17448) covalent geometry : angle 0.41125 (23958) hydrogen bonds : bond 0.03015 ( 643) hydrogen bonds : angle 4.71331 ( 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 192 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.678 Fit side-chains REVERT: A 18 GLN cc_start: 0.8777 (mt0) cc_final: 0.8430 (mp10) REVERT: A 188 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: A 199 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8087 (p0) REVERT: A 200 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 204 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8389 (mptp) REVERT: A 215 GLU cc_start: 0.7917 (tt0) cc_final: 0.7454 (tp30) REVERT: A 232 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: B 64 LYS cc_start: 0.8082 (mptt) cc_final: 0.7764 (mptp) REVERT: B 204 LYS cc_start: 0.8126 (mttp) cc_final: 0.7353 (mmpt) REVERT: B 258 PHE cc_start: 0.7763 (t80) cc_final: 0.7440 (t80) REVERT: C 149 LYS cc_start: 0.8076 (mttt) cc_final: 0.7660 (mppt) REVERT: C 264 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: D 68 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: D 103 SER cc_start: 0.8007 (p) cc_final: 0.7640 (m) REVERT: D 173 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7868 (tttt) REVERT: D 264 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6575 (tt0) REVERT: E 166 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8635 (m) REVERT: E 202 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6884 (mt-10) REVERT: E 251 LEU cc_start: 0.7794 (tp) cc_final: 0.7521 (tp) REVERT: E 263 PHE cc_start: 0.7812 (p90) cc_final: 0.7560 (p90) REVERT: E 284 GLN cc_start: 0.7318 (tt0) cc_final: 0.6449 (tp40) REVERT: E 330 MET cc_start: 0.5950 (tpp) cc_final: 0.5683 (ttt) REVERT: F 68 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: F 138 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7473 (mtp85) REVERT: F 144 THR cc_start: 0.8768 (m) cc_final: 0.8404 (p) REVERT: F 188 GLN cc_start: 0.8002 (tt0) cc_final: 0.7586 (tp40) REVERT: F 191 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7215 (mp0) REVERT: F 264 GLU cc_start: 0.6479 (mm-30) cc_final: 0.5549 (tt0) outliers start: 43 outliers final: 16 residues processed: 182 average time/residue: 0.6159 time to fit residues: 125.9435 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 325 THR Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU 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 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 169 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 172 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN E 136 ASN F 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132667 restraints weight = 17016.505| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.57 r_work: 0.3022 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0969 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= 0.100 Angle : 0.436 5.941 23958 Z= 0.237 Chirality : 0.043 0.142 2814 Planarity : 0.003 0.040 2848 Dihedral : 10.614 73.523 2996 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.12 % Allowed : 14.41 % 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: 0.50 (0.19), residues: 1971 helix: 1.25 (0.24), residues: 509 sheet: 1.49 (0.29), residues: 341 loop : -0.47 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 90 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 covalent geometry : bond 0.00233 (17448) covalent geometry : angle 0.43630 (23958) hydrogen bonds : bond 0.03401 ( 643) hydrogen bonds : angle 4.77859 ( 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: 55 poor density : 141 time to evaluate : 0.693 Fit side-chains REVERT: A 18 GLN cc_start: 0.8799 (mt0) cc_final: 0.8456 (mp10) REVERT: A 188 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: A 199 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8160 (p0) REVERT: A 200 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 204 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8391 (mptp) REVERT: A 215 GLU cc_start: 0.7939 (tt0) cc_final: 0.7455 (tp30) REVERT: A 232 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: B 64 LYS cc_start: 0.8204 (mptt) cc_final: 0.7866 (mptp) REVERT: B 204 LYS cc_start: 0.8119 (mttp) cc_final: 0.7340 (mmpt) REVERT: B 258 PHE cc_start: 0.7805 (t80) cc_final: 0.7481 (t80) REVERT: C 149 LYS cc_start: 0.8067 (mttt) cc_final: 0.7649 (mppt) REVERT: C 264 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: D 68 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: D 173 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8014 (tttt) REVERT: D 264 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6562 (tt0) REVERT: E 46 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8697 (mptp) REVERT: E 166 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8639 (m) REVERT: E 202 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6924 (mt-10) REVERT: E 251 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7539 (tp) REVERT: E 263 PHE cc_start: 0.7796 (p90) cc_final: 0.7567 (p90) REVERT: E 284 GLN cc_start: 0.7327 (tt0) cc_final: 0.6457 (tp40) REVERT: E 330 MET cc_start: 0.5949 (tpp) cc_final: 0.5659 (ttt) REVERT: F 21 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: F 68 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: F 110 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6738 (mtpt) REVERT: F 138 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7505 (mtp85) REVERT: F 144 THR cc_start: 0.8798 (m) cc_final: 0.8434 (p) REVERT: F 167 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (pp) REVERT: F 188 GLN cc_start: 0.7992 (tt0) cc_final: 0.7586 (tp-100) REVERT: F 191 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7221 (mp0) REVERT: F 213 PHE cc_start: 0.5875 (t80) cc_final: 0.5656 (t80) REVERT: F 245 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7033 (tt) REVERT: F 264 GLU cc_start: 0.6532 (mm-30) cc_final: 0.5624 (tt0) outliers start: 55 outliers final: 20 residues processed: 185 average time/residue: 0.6385 time to fit residues: 131.9203 Evaluate side-chains 175 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 325 THR 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 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 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 46 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 180 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 179 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4003 r_free = 0.4003 target = 0.176898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128818 restraints weight = 16938.739| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.82 r_work: 0.3035 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1088 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= 0.123 Angle : 0.468 5.498 23958 Z= 0.254 Chirality : 0.044 0.147 2814 Planarity : 0.004 0.042 2848 Dihedral : 10.703 73.604 2996 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.06 % Allowed : 14.69 % Favored : 82.25 % 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: 0.36 (0.18), residues: 1971 helix: 1.11 (0.24), residues: 509 sheet: 1.34 (0.28), residues: 348 loop : -0.53 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.012 0.001 TYR A 342 PHE 0.014 0.001 PHE F 268 TRP 0.012 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00293 (17448) covalent geometry : angle 0.46816 (23958) hydrogen bonds : bond 0.03787 ( 643) hydrogen bonds : angle 4.90185 ( 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: 54 poor density : 132 time to evaluate : 0.513 Fit side-chains REVERT: A 18 GLN cc_start: 0.8917 (mt0) cc_final: 0.8430 (mp10) REVERT: A 21 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: A 188 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: A 199 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8293 (p0) REVERT: A 200 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 204 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8390 (mptp) REVERT: A 215 GLU cc_start: 0.7999 (tt0) cc_final: 0.7389 (tp30) REVERT: A 232 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: B 191 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: B 204 LYS cc_start: 0.8076 (mttp) cc_final: 0.7256 (mmpt) REVERT: B 258 PHE cc_start: 0.7673 (t80) cc_final: 0.7356 (t80) REVERT: C 149 LYS cc_start: 0.8161 (mttt) cc_final: 0.7602 (mppt) REVERT: C 188 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7972 (mm110) REVERT: C 264 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: D 68 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: D 173 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8053 (tttt) REVERT: D 264 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6379 (tt0) REVERT: E 46 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8775 (mptp) REVERT: E 166 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8683 (m) REVERT: E 202 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6928 (mt-10) REVERT: E 251 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7486 (tp) REVERT: E 263 PHE cc_start: 0.7803 (p90) cc_final: 0.7541 (p90) REVERT: E 284 GLN cc_start: 0.7226 (tt0) cc_final: 0.6317 (tp40) REVERT: E 330 MET cc_start: 0.5877 (tpp) cc_final: 0.5638 (ttt) REVERT: F 21 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: F 68 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: F 110 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6773 (mtpt) REVERT: F 138 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7483 (mtp85) REVERT: F 144 THR cc_start: 0.8824 (m) cc_final: 0.8374 (p) REVERT: F 167 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8309 (pp) REVERT: F 191 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7201 (mp0) REVERT: F 245 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6858 (tt) REVERT: F 264 GLU cc_start: 0.6469 (mm-30) cc_final: 0.5558 (tt0) outliers start: 54 outliers final: 22 residues processed: 176 average time/residue: 0.6415 time to fit residues: 125.4963 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 96 ILE Chi-restraints excluded: chain B residue 191 GLU 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 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 166 THR 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 325 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 44 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 175 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4006 r_free = 0.4006 target = 0.177091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128906 restraints weight = 16936.870| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.77 r_work: 0.3053 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1112 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= 0.118 Angle : 0.459 5.366 23958 Z= 0.249 Chirality : 0.044 0.145 2814 Planarity : 0.004 0.041 2848 Dihedral : 10.702 73.607 2996 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.06 % Allowed : 14.92 % Favored : 82.02 % 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: 0.34 (0.18), residues: 1971 helix: 1.09 (0.24), residues: 509 sheet: 1.36 (0.28), residues: 346 loop : -0.55 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.011 0.001 TYR A 342 PHE 0.014 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 covalent geometry : bond 0.00280 (17448) covalent geometry : angle 0.45855 (23958) hydrogen bonds : bond 0.03636 ( 643) hydrogen bonds : angle 4.88022 ( 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 185 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.640 Fit side-chains REVERT: A 18 GLN cc_start: 0.8857 (mt0) cc_final: 0.8353 (mp10) REVERT: A 188 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: A 199 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8214 (p0) REVERT: A 200 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8213 (mp) REVERT: A 204 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8363 (mptp) REVERT: A 215 GLU cc_start: 0.7933 (tt0) cc_final: 0.7310 (tp30) REVERT: A 232 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: B 191 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: B 204 LYS cc_start: 0.8044 (mttp) cc_final: 0.7217 (mmpt) REVERT: B 258 PHE cc_start: 0.7597 (t80) cc_final: 0.7321 (t80) REVERT: C 149 LYS cc_start: 0.8145 (mttt) cc_final: 0.7560 (mppt) REVERT: C 188 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7957 (tp40) REVERT: C 264 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: D 68 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: D 173 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8034 (tttt) REVERT: D 264 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6315 (tt0) REVERT: E 46 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8761 (mptp) REVERT: E 166 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8675 (m) REVERT: E 251 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7422 (tp) REVERT: E 263 PHE cc_start: 0.7787 (p90) cc_final: 0.7517 (p90) REVERT: E 284 GLN cc_start: 0.7175 (tt0) cc_final: 0.6267 (tp40) REVERT: E 330 MET cc_start: 0.5840 (tpp) cc_final: 0.5591 (ttt) REVERT: F 21 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: F 68 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: F 110 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6723 (mtpt) REVERT: F 138 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7411 (mtp85) REVERT: F 144 THR cc_start: 0.8801 (m) cc_final: 0.8330 (p) REVERT: F 167 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8260 (pp) REVERT: F 191 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7174 (mp0) REVERT: F 264 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5498 (tt0) outliers start: 54 outliers final: 24 residues processed: 173 average time/residue: 0.6262 time to fit residues: 120.8603 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 325 THR 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 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 304 GLU 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 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 166 THR 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 110 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3974 r_free = 0.3974 target = 0.174334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129257 restraints weight = 17048.564| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.66 r_work: 0.2996 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17448 Z= 0.172 Angle : 0.525 5.952 23958 Z= 0.283 Chirality : 0.046 0.151 2814 Planarity : 0.004 0.054 2848 Dihedral : 10.826 73.683 2994 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.95 % Allowed : 15.48 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 1971 helix: 0.89 (0.24), residues: 509 sheet: 1.26 (0.28), residues: 343 loop : -0.68 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 90 TYR 0.016 0.001 TYR A 342 PHE 0.017 0.002 PHE F 268 TRP 0.011 0.001 TRP E 332 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00422 (17448) covalent geometry : angle 0.52492 (23958) hydrogen bonds : bond 0.04388 ( 643) hydrogen bonds : angle 5.10153 ( 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 182 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.629 Fit side-chains REVERT: A 18 GLN cc_start: 0.8946 (mt0) cc_final: 0.8444 (mp10) REVERT: A 199 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8314 (p0) REVERT: A 200 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 204 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8447 (mptp) REVERT: A 215 GLU cc_start: 0.8037 (tt0) cc_final: 0.7369 (tp30) REVERT: A 232 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: B 191 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: B 200 LEU cc_start: 0.7534 (mt) cc_final: 0.7317 (tp) REVERT: B 204 LYS cc_start: 0.8059 (mttp) cc_final: 0.7235 (mmpt) REVERT: B 258 PHE cc_start: 0.7672 (t80) cc_final: 0.7385 (t80) REVERT: C 149 LYS cc_start: 0.8209 (mttt) cc_final: 0.7625 (mppt) REVERT: C 188 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8013 (tp-100) REVERT: C 264 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7083 (mm-30) REVERT: D 68 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: D 104 MET cc_start: 0.7872 (mmm) cc_final: 0.7671 (mmt) REVERT: D 138 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7749 (ttt-90) REVERT: D 173 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8064 (tttt) REVERT: D 264 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6363 (tt0) REVERT: E 46 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8820 (mptp) REVERT: E 166 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8676 (m) REVERT: E 251 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7552 (tp) REVERT: E 263 PHE cc_start: 0.7827 (p90) cc_final: 0.7594 (p90) REVERT: E 284 GLN cc_start: 0.7214 (tt0) cc_final: 0.6326 (tp40) REVERT: E 330 MET cc_start: 0.5762 (tpp) cc_final: 0.5552 (ttt) REVERT: F 21 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: F 138 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7468 (mtp85) REVERT: F 144 THR cc_start: 0.8838 (m) cc_final: 0.8350 (p) REVERT: F 191 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7313 (mp0) REVERT: F 264 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5591 (tt0) outliers start: 52 outliers final: 27 residues processed: 173 average time/residue: 0.6385 time to fit residues: 123.1995 Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 325 THR 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 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 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 166 THR 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 10 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 3 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 200 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4000 r_free = 0.4000 target = 0.176792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130359 restraints weight = 17062.011| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.86 r_work: 0.3046 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17448 Z= 0.090 Angle : 0.433 5.095 23958 Z= 0.236 Chirality : 0.043 0.143 2814 Planarity : 0.003 0.040 2848 Dihedral : 10.666 73.620 2994 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.16 % Allowed : 16.34 % 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: 0.35 (0.18), residues: 1971 helix: 1.13 (0.24), residues: 509 sheet: 1.35 (0.28), residues: 346 loop : -0.56 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.008 0.001 TYR A 342 PHE 0.010 0.001 PHE F 268 TRP 0.008 0.001 TRP E 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00201 (17448) covalent geometry : angle 0.43251 (23958) hydrogen bonds : bond 0.03270 ( 643) hydrogen bonds : angle 4.82294 ( 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 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.647 Fit side-chains REVERT: A 18 GLN cc_start: 0.8777 (mt0) cc_final: 0.8443 (mp10) REVERT: A 188 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 199 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8126 (p0) REVERT: A 200 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 204 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8392 (mptp) REVERT: A 215 GLU cc_start: 0.7880 (tt0) cc_final: 0.7444 (tp30) REVERT: A 232 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: B 191 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: B 204 LYS cc_start: 0.8097 (mttp) cc_final: 0.7319 (mmpt) REVERT: B 258 PHE cc_start: 0.7779 (t80) cc_final: 0.7492 (t80) REVERT: C 149 LYS cc_start: 0.8105 (mttt) cc_final: 0.7654 (mppt) REVERT: C 264 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: D 68 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: D 173 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7850 (tttt) REVERT: D 264 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6484 (tt0) REVERT: E 46 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8651 (mptp) REVERT: E 166 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8614 (m) REVERT: E 167 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7907 (pp) REVERT: E 251 LEU cc_start: 0.7838 (tp) cc_final: 0.7563 (tp) REVERT: E 263 PHE cc_start: 0.7839 (p90) cc_final: 0.7638 (p90) REVERT: E 284 GLN cc_start: 0.7320 (tt0) cc_final: 0.6500 (tp40) REVERT: E 330 MET cc_start: 0.5981 (tpp) cc_final: 0.5731 (ttt) REVERT: F 21 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: F 68 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: F 138 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7485 (mtp85) REVERT: F 144 THR cc_start: 0.8813 (m) cc_final: 0.8439 (p) REVERT: F 167 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8370 (pp) REVERT: F 191 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7377 (mp0) REVERT: F 213 PHE cc_start: 0.5944 (t80) cc_final: 0.5640 (t80) REVERT: F 264 GLU cc_start: 0.6503 (mm-30) cc_final: 0.5623 (tt0) outliers start: 38 outliers final: 21 residues processed: 162 average time/residue: 0.6488 time to fit residues: 116.9359 Evaluate side-chains 166 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 191 GLU 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 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 46 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 189 LEU 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 149 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3979 r_free = 0.3979 target = 0.174782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130840 restraints weight = 16940.607| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.80 r_work: 0.2987 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17448 Z= 0.152 Angle : 0.503 5.423 23958 Z= 0.271 Chirality : 0.045 0.150 2814 Planarity : 0.004 0.048 2848 Dihedral : 10.787 73.683 2994 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.38 % Allowed : 16.28 % Favored : 81.34 % 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: 0.18 (0.18), residues: 1971 helix: 1.01 (0.24), residues: 506 sheet: 1.27 (0.29), residues: 343 loop : -0.67 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 138 TYR 0.013 0.001 TYR A 342 PHE 0.016 0.002 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00370 (17448) covalent geometry : angle 0.50273 (23958) hydrogen bonds : bond 0.04114 ( 643) hydrogen bonds : angle 5.02749 ( 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 171 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.641 Fit side-chains REVERT: A 18 GLN cc_start: 0.8831 (mt0) cc_final: 0.8460 (mp10) REVERT: A 188 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 199 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8214 (p0) REVERT: A 200 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 204 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8449 (mptp) REVERT: A 215 GLU cc_start: 0.7917 (tt0) cc_final: 0.7421 (tp30) REVERT: A 232 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 191 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: B 204 LYS cc_start: 0.8088 (mttp) cc_final: 0.7293 (mmpt) REVERT: B 258 PHE cc_start: 0.7770 (t80) cc_final: 0.7465 (t80) REVERT: C 149 LYS cc_start: 0.8181 (mttt) cc_final: 0.7694 (mppt) REVERT: C 188 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8057 (tp-100) REVERT: C 264 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7107 (mm-30) REVERT: D 68 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: D 104 MET cc_start: 0.7989 (mmm) cc_final: 0.7761 (mmt) REVERT: D 173 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8046 (tttt) REVERT: D 264 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6420 (tt0) REVERT: E 46 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8701 (mptp) REVERT: E 136 ASN cc_start: 0.8329 (m110) cc_final: 0.8117 (m-40) REVERT: E 166 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8644 (m) REVERT: E 251 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7592 (tp) REVERT: E 263 PHE cc_start: 0.7846 (p90) cc_final: 0.7632 (p90) REVERT: E 284 GLN cc_start: 0.7322 (tt0) cc_final: 0.6479 (tp40) REVERT: E 330 MET cc_start: 0.5890 (tpp) cc_final: 0.5648 (ttt) REVERT: F 21 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: F 68 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: F 110 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7028 (mtpt) REVERT: F 138 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7514 (mtp85) REVERT: F 144 THR cc_start: 0.8833 (m) cc_final: 0.8411 (p) REVERT: F 191 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7343 (mp0) REVERT: F 264 GLU cc_start: 0.6522 (mm-30) cc_final: 0.5656 (tt0) outliers start: 42 outliers final: 21 residues processed: 164 average time/residue: 0.6492 time to fit residues: 118.6419 Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 191 GLU 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 245 LEU 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 46 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR 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 10 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3978 r_free = 0.3978 target = 0.174733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129683 restraints weight = 16955.746| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.68 r_work: 0.2996 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17448 Z= 0.151 Angle : 0.503 5.207 23958 Z= 0.272 Chirality : 0.045 0.148 2814 Planarity : 0.004 0.048 2848 Dihedral : 10.855 73.719 2994 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.27 % Allowed : 16.39 % Favored : 81.34 % 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: 0.09 (0.18), residues: 1971 helix: 0.89 (0.24), residues: 509 sheet: 1.16 (0.28), residues: 348 loop : -0.69 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 138 TYR 0.014 0.001 TYR A 342 PHE 0.015 0.002 PHE F 268 TRP 0.008 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00366 (17448) covalent geometry : angle 0.50294 (23958) hydrogen bonds : bond 0.04126 ( 643) hydrogen bonds : angle 5.06576 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.84 seconds wall clock time: 107 minutes 32.98 seconds (6452.98 seconds total)