Starting phenix.real_space_refine on Thu Aug 6 21:23:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m48_63618/08_2026/9m48_63618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m48_63618/08_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_63618/08_2026/9m48_63618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m48_63618/08_2026/9m48_63618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m48_63618/08_2026/9m48_63618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m48_63618/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16978 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain: "B" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2705 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "C" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "D" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2091 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 2 Chain: "E" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "G" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.80, per 1000 atoms: 0.22 Number of scatterers: 16978 At special positions: 0 Unit cell: (120.96, 124.32, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 1 26.99 S 56 16.00 P 62 15.00 O 3428 8.00 N 2770 7.00 C 10661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 825.4 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: 2.60 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: 3.23 Time building geometry restraints manager: 2.04 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: 23555 1.57 - 3.15: 384 3.15 - 4.72: 17 4.72 - 6.29: 1 6.29 - 7.87: 1 Bond angle restraints: 23958 Sorted by residual: angle pdb=" O5' C H 29 " pdb=" C5' C H 29 " pdb=" C4' C H 29 " ideal model delta sigma weight residual 109.40 111.87 -2.47 8.00e-01 1.56e+00 9.52e+00 angle pdb=" O5' A G 3 " pdb=" C5' A G 3 " pdb=" C4' A G 3 " ideal model delta sigma weight residual 109.40 111.85 -2.45 8.00e-01 1.56e+00 9.35e+00 angle pdb=" O5' G G 4 " pdb=" C5' G G 4 " pdb=" C4' G G 4 " ideal model delta sigma weight residual 109.40 111.84 -2.44 8.00e-01 1.56e+00 9.31e+00 angle pdb=" O5' U G 5 " pdb=" C5' U G 5 " pdb=" C4' U G 5 " ideal model delta sigma weight residual 109.40 111.80 -2.40 8.00e-01 1.56e+00 9.02e+00 angle pdb=" O5' A G 11 " pdb=" C5' A G 11 " pdb=" C4' A G 11 " ideal model delta sigma weight residual 109.40 111.78 -2.38 8.00e-01 1.56e+00 8.86e+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 - 0.028: 1742 0.028 - 0.057: 577 0.057 - 0.085: 209 0.085 - 0.113: 186 0.113 - 0.142: 100 Chirality restraints: 2814 Sorted by residual: chirality pdb=" C2' G G 10 " pdb=" C3' G G 10 " pdb=" O2' G G 10 " pdb=" C1' G G 10 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" C2' U G 14 " pdb=" C3' U G 14 " pdb=" O2' U G 14 " pdb=" C1' U G 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" C2' A G 11 " pdb=" C3' A G 11 " pdb=" O2' A G 11 " pdb=" C1' A G 11 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.80e-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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.260 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17448 Z= 0.094 Angle : 0.457 7.867 23958 Z= 0.286 Chirality : 0.046 0.142 2814 Planarity : 0.003 0.041 2848 Dihedral : 15.711 89.314 6743 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.02 % Allowed : 16.28 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1971 helix: 1.38 (0.24), residues: 509 sheet: 1.44 (0.30), residues: 328 loop : -0.47 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 138 TYR 0.007 0.001 TYR C 225 PHE 0.010 0.001 PHE F 7 TRP 0.003 0.001 TRP E 332 HIS 0.003 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.09 (17448) covalent geometry : angle 0.45683 / 0.29 (23958) hydrogen bonds : bond 0.14172 / 9.50 ( 643) hydrogen bonds : angle 6.35742 / 4.56 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.653 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: 0.6250 time to fit residues: 112.0257 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 : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131841 restraints weight = 17049.512| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.57 r_work: 0.3028 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17448 Z= 0.115 Angle : 0.458 7.230 23958 Z= 0.252 Chirality : 0.043 0.144 2814 Planarity : 0.004 0.040 2848 Dihedral : 10.742 73.517 3016 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.18 % Allowed : 14.24 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1971 helix: 1.25 (0.24), residues: 509 sheet: 1.35 (0.29), residues: 335 loop : -0.49 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.009 0.001 TYR F 342 PHE 0.014 0.001 PHE F 268 TRP 0.009 0.001 TRP E 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (17448) covalent geometry : angle 0.45771 / 0.25 (23958) hydrogen bonds : bond 0.04184 / 2.77 ( 643) hydrogen bonds : angle 5.31016 / 3.76 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.702 Fit side-chains REVERT: A 18 GLN cc_start: 0.8776 (mt0) cc_final: 0.8421 (mp10) REVERT: A 36 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6456 (t0) REVERT: A 199 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8108 (p0) REVERT: A 200 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 204 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8440 (mptp) REVERT: A 215 GLU cc_start: 0.7869 (tt0) cc_final: 0.7355 (tp30) REVERT: A 232 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: A 330 MET cc_start: 0.8670 (tpp) cc_final: 0.7902 (tpt) REVERT: B 64 LYS cc_start: 0.8142 (mptt) cc_final: 0.7802 (mptp) REVERT: B 204 LYS cc_start: 0.8114 (mttp) cc_final: 0.7344 (mmpt) REVERT: B 258 PHE cc_start: 0.7823 (t80) cc_final: 0.7471 (t80) REVERT: B 317 VAL cc_start: 0.7794 (t) cc_final: 0.7590 (p) REVERT: C 149 LYS cc_start: 0.8041 (mttt) cc_final: 0.7636 (mppt) REVERT: C 264 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: D 68 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: D 103 SER cc_start: 0.8027 (p) cc_final: 0.7615 (m) REVERT: D 173 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8026 (tttt) REVERT: E 202 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6828 (mt-10) REVERT: E 251 LEU cc_start: 0.7790 (tp) cc_final: 0.7564 (tp) REVERT: E 263 PHE cc_start: 0.7764 (p90) cc_final: 0.7518 (p90) REVERT: E 284 GLN cc_start: 0.7138 (tt0) cc_final: 0.6355 (tp40) REVERT: E 330 MET cc_start: 0.5858 (tpp) cc_final: 0.5566 (ttt) REVERT: F 21 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: F 68 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: F 138 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7570 (mtp85) REVERT: F 144 THR cc_start: 0.8828 (m) cc_final: 0.8482 (p) REVERT: F 188 GLN cc_start: 0.7983 (tt0) cc_final: 0.7597 (tp-100) REVERT: F 191 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7278 (mp0) outliers start: 56 outliers final: 20 residues processed: 186 average time/residue: 0.6001 time to fit residues: 125.3565 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 95 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN 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 = 0.4001 r_free = 0.4001 target = 0.176845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128998 restraints weight = 17181.041| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.01 r_work: 0.3055 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17448 Z= 0.107 Angle : 0.444 6.702 23958 Z= 0.243 Chirality : 0.043 0.143 2814 Planarity : 0.003 0.039 2848 Dihedral : 10.703 73.430 3003 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.01 % Allowed : 14.46 % 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: 0.42 (0.18), residues: 1971 helix: 1.20 (0.24), residues: 509 sheet: 1.49 (0.29), residues: 328 loop : -0.52 (0.17), residues: 1134 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 0.011 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17448) covalent geometry : angle 0.44361 / 0.24 (23958) hydrogen bonds : bond 0.03880 / 2.57 ( 643) hydrogen bonds : angle 5.05828 / 3.57 ( 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 198 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.674 Fit side-chains REVERT: A 18 GLN cc_start: 0.8830 (mt0) cc_final: 0.8348 (mp10) REVERT: A 200 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 204 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8401 (mptp) REVERT: A 215 GLU cc_start: 0.7949 (tt0) cc_final: 0.7277 (tp30) REVERT: A 232 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: B 204 LYS cc_start: 0.8037 (mttp) cc_final: 0.7220 (mmpt) REVERT: B 258 PHE cc_start: 0.7639 (t80) cc_final: 0.7291 (t80) REVERT: B 317 VAL cc_start: 0.7782 (t) cc_final: 0.7560 (p) REVERT: C 149 LYS cc_start: 0.8084 (mttt) cc_final: 0.7545 (mppt) REVERT: C 264 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: D 68 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: D 103 SER cc_start: 0.7933 (p) cc_final: 0.7536 (m) REVERT: D 173 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7943 (tttt) REVERT: E 202 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6837 (mt-10) REVERT: E 251 LEU cc_start: 0.7700 (tp) cc_final: 0.7445 (tp) REVERT: E 263 PHE cc_start: 0.7785 (p90) cc_final: 0.7551 (p90) REVERT: E 284 GLN cc_start: 0.7108 (tt0) cc_final: 0.6170 (tp40) REVERT: E 330 MET cc_start: 0.5810 (tpp) cc_final: 0.5575 (ttt) REVERT: F 21 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: F 68 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: F 138 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7361 (mtp85) REVERT: F 144 THR cc_start: 0.8797 (m) cc_final: 0.8327 (p) REVERT: F 188 GLN cc_start: 0.7999 (tt0) cc_final: 0.7485 (tp-100) REVERT: F 191 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7154 (mp0) REVERT: F 264 GLU cc_start: 0.6482 (mm-30) cc_final: 0.5538 (tt0) outliers start: 53 outliers final: 21 residues processed: 187 average time/residue: 0.5800 time to fit residues: 121.9757 Evaluate side-chains 167 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 51 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4020 r_free = 0.4020 target = 0.178414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130265 restraints weight = 17106.678| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.89 r_work: 0.3076 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0759 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= 0.091 Angle : 0.423 6.623 23958 Z= 0.232 Chirality : 0.042 0.140 2814 Planarity : 0.003 0.037 2848 Dihedral : 10.636 73.442 2998 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 1971 helix: 1.26 (0.24), residues: 509 sheet: 1.60 (0.29), residues: 326 loop : -0.50 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 257 TYR 0.008 0.001 TYR A 342 PHE 0.011 0.001 PHE F 268 TRP 0.011 0.001 TRP E 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (17448) covalent geometry : angle 0.42260 / 0.23 (23958) hydrogen bonds : bond 0.03464 / 2.31 ( 643) hydrogen bonds : angle 4.90919 / 3.46 ( 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 190 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.672 Fit side-chains REVERT: A 18 GLN cc_start: 0.8824 (mt0) cc_final: 0.8375 (mp10) REVERT: A 188 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: A 199 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8148 (p0) REVERT: A 200 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 204 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8386 (mptp) REVERT: A 215 GLU cc_start: 0.7962 (tt0) cc_final: 0.7310 (tp30) REVERT: A 232 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: B 64 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7817 (mptp) REVERT: B 200 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7062 (tp) REVERT: B 204 LYS cc_start: 0.8053 (mttp) cc_final: 0.7244 (mmpt) REVERT: B 258 PHE cc_start: 0.7669 (t80) cc_final: 0.7316 (t80) REVERT: B 317 VAL cc_start: 0.7829 (t) cc_final: 0.7621 (p) REVERT: C 149 LYS cc_start: 0.8083 (mttt) cc_final: 0.7557 (mppt) REVERT: C 264 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: D 68 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: D 103 SER cc_start: 0.7930 (p) cc_final: 0.7523 (m) REVERT: D 173 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7956 (tttt) REVERT: E 202 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6885 (mt-10) REVERT: E 251 LEU cc_start: 0.7772 (tp) cc_final: 0.7494 (tp) REVERT: E 263 PHE cc_start: 0.7763 (p90) cc_final: 0.7504 (p90) REVERT: E 284 GLN cc_start: 0.7121 (tt0) cc_final: 0.6183 (tp40) REVERT: E 330 MET cc_start: 0.5830 (tpp) cc_final: 0.5616 (ttt) REVERT: F 21 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: F 68 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: F 138 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7386 (mtp85) REVERT: F 144 THR cc_start: 0.8806 (m) cc_final: 0.8355 (p) REVERT: F 188 GLN cc_start: 0.8008 (tt0) cc_final: 0.7509 (tp-100) REVERT: F 191 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7227 (mp0) REVERT: F 264 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5531 (tt0) outliers start: 47 outliers final: 23 residues processed: 179 average time/residue: 0.5989 time to fit residues: 120.2847 Evaluate side-chains 174 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL 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: 0.0970 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 174 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4015 r_free = 0.4015 target = 0.178182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133531 restraints weight = 17066.444| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.65 r_work: 0.3042 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17448 Z= 0.079 Angle : 0.407 5.987 23958 Z= 0.225 Chirality : 0.042 0.138 2814 Planarity : 0.003 0.037 2848 Dihedral : 10.588 73.433 2996 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.89 % Allowed : 14.97 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1971 helix: 1.32 (0.24), residues: 509 sheet: 1.69 (0.29), residues: 326 loop : -0.45 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 257 TYR 0.007 0.001 TYR C 225 PHE 0.010 0.001 PHE E 7 TRP 0.009 0.001 TRP E 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (17448) covalent geometry : angle 0.40687 / 0.22 (23958) hydrogen bonds : bond 0.03167 / 2.11 ( 643) hydrogen bonds : angle 4.77820 / 3.37 ( 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 200 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.649 Fit side-chains REVERT: A 18 GLN cc_start: 0.8772 (mt0) cc_final: 0.8435 (mp10) REVERT: A 188 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: A 199 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8081 (p0) REVERT: A 200 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 204 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8406 (mptp) REVERT: A 215 GLU cc_start: 0.7906 (tt0) cc_final: 0.7411 (tp30) REVERT: A 232 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: B 64 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7765 (mptp) REVERT: B 204 LYS cc_start: 0.8118 (mttp) cc_final: 0.7345 (mmpt) REVERT: B 258 PHE cc_start: 0.7805 (t80) cc_final: 0.7493 (t80) REVERT: B 317 VAL cc_start: 0.7884 (t) cc_final: 0.7679 (p) REVERT: C 149 LYS cc_start: 0.8044 (mttt) cc_final: 0.7645 (mppt) REVERT: C 264 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: D 68 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: D 103 SER cc_start: 0.8000 (p) cc_final: 0.7601 (m) REVERT: D 173 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7889 (tttt) REVERT: E 165 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8290 (m) REVERT: E 251 LEU cc_start: 0.7822 (tp) cc_final: 0.7558 (tp) REVERT: E 263 PHE cc_start: 0.7811 (p90) cc_final: 0.7574 (p90) REVERT: E 284 GLN cc_start: 0.7227 (tt0) cc_final: 0.6385 (tp40) REVERT: E 330 MET cc_start: 0.5954 (tpp) cc_final: 0.5675 (ttt) REVERT: F 68 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: F 138 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7474 (mtp85) REVERT: F 144 THR cc_start: 0.8801 (m) cc_final: 0.8428 (p) REVERT: F 188 GLN cc_start: 0.7957 (tt0) cc_final: 0.7551 (tp40) REVERT: F 191 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7212 (mp0) REVERT: F 264 GLU cc_start: 0.6479 (mm-30) cc_final: 0.5654 (tt0) outliers start: 51 outliers final: 22 residues processed: 188 average time/residue: 0.6149 time to fit residues: 130.1440 Evaluate side-chains 175 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 115 ILE 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 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 B residue 303 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3999 r_free = 0.3999 target = 0.176425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128357 restraints weight = 16925.252| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.73 r_work: 0.3037 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17448 Z= 0.160 Angle : 0.492 5.971 23958 Z= 0.268 Chirality : 0.045 0.150 2814 Planarity : 0.004 0.054 2848 Dihedral : 10.721 73.565 2996 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.18 % Allowed : 15.20 % Favored : 81.62 % 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: 0.31 (0.18), residues: 1971 helix: 1.12 (0.24), residues: 506 sheet: 1.49 (0.29), residues: 331 loop : -0.62 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.012 0.001 TYR A 342 PHE 0.017 0.002 PHE F 268 TRP 0.011 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (17448) covalent geometry : angle 0.49239 / 0.27 (23958) hydrogen bonds : bond 0.04189 / 2.75 ( 643) hydrogen bonds : angle 5.02819 / 3.54 ( 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 188 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 0.421 Fit side-chains REVERT: A 18 GLN cc_start: 0.8886 (mt0) cc_final: 0.8442 (mp10) REVERT: A 199 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8241 (p0) REVERT: A 200 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (mp) REVERT: A 204 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8421 (mptp) REVERT: A 215 GLU cc_start: 0.7987 (tt0) cc_final: 0.7314 (tp30) REVERT: A 232 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: B 204 LYS cc_start: 0.8082 (mttp) cc_final: 0.7272 (mmpt) REVERT: B 258 PHE cc_start: 0.7696 (t80) cc_final: 0.7361 (t80) REVERT: B 317 VAL cc_start: 0.7879 (t) cc_final: 0.7656 (p) REVERT: C 149 LYS cc_start: 0.8159 (mttt) cc_final: 0.7597 (mppt) REVERT: C 188 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: C 264 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: D 68 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: D 103 SER cc_start: 0.8006 (p) cc_final: 0.7603 (m) REVERT: D 173 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8122 (tttt) REVERT: E 251 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7586 (tp) REVERT: E 263 PHE cc_start: 0.7861 (p90) cc_final: 0.7646 (p90) REVERT: E 284 GLN cc_start: 0.7175 (tt0) cc_final: 0.6237 (tp40) REVERT: E 330 MET cc_start: 0.5761 (tpp) cc_final: 0.5509 (ttt) REVERT: F 21 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: F 68 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: F 138 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7498 (mtp85) REVERT: F 144 THR cc_start: 0.8817 (m) cc_final: 0.8360 (p) REVERT: F 191 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7237 (mp0) REVERT: F 264 GLU cc_start: 0.6531 (mm-30) cc_final: 0.5578 (tt0) outliers start: 56 outliers final: 29 residues processed: 176 average time/residue: 0.5132 time to fit residues: 101.7670 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL 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 10 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 44 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 162 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 198 optimal weight: 30.0000 chunk 120 optimal weight: 0.0980 chunk 175 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.177692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130573 restraints weight = 16999.776| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.96 r_work: 0.3068 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17448 Z= 0.079 Angle : 0.411 5.793 23958 Z= 0.227 Chirality : 0.042 0.137 2814 Planarity : 0.003 0.037 2848 Dihedral : 10.630 73.465 2996 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 16.34 % Favored : 81.62 % 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 (0.18), residues: 1971 helix: 1.29 (0.24), residues: 509 sheet: 1.64 (0.29), residues: 326 loop : -0.51 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.008 0.001 TYR B 193 PHE 0.009 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/Z covalent geometry : bond 0.00171 / 0.08 (17448) covalent geometry : angle 0.41058 / 0.23 (23958) hydrogen bonds : bond 0.03152 / 2.11 ( 643) hydrogen bonds : angle 4.77071 / 3.37 ( 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 173 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.429 Fit side-chains REVERT: A 18 GLN cc_start: 0.8815 (mt0) cc_final: 0.8374 (mp10) REVERT: A 188 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: A 199 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8190 (p0) REVERT: A 200 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 204 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8378 (mptp) REVERT: A 215 GLU cc_start: 0.7986 (tt0) cc_final: 0.7332 (tp30) REVERT: A 232 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: B 64 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7857 (mptp) REVERT: B 200 LEU cc_start: 0.7262 (tp) cc_final: 0.7021 (mt) REVERT: B 204 LYS cc_start: 0.8057 (mttp) cc_final: 0.7242 (mmpt) REVERT: B 258 PHE cc_start: 0.7616 (t80) cc_final: 0.7337 (t80) REVERT: B 317 VAL cc_start: 0.7826 (t) cc_final: 0.7604 (p) REVERT: C 149 LYS cc_start: 0.8098 (mttt) cc_final: 0.7585 (mppt) REVERT: C 264 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: D 68 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: D 103 SER cc_start: 0.8026 (p) cc_final: 0.7627 (m) REVERT: D 104 MET cc_start: 0.7999 (mmm) cc_final: 0.7790 (mmt) REVERT: D 173 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7883 (tttt) REVERT: E 251 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7489 (tp) REVERT: E 263 PHE cc_start: 0.7811 (p90) cc_final: 0.7549 (p90) REVERT: E 284 GLN cc_start: 0.7105 (tt0) cc_final: 0.6230 (tp40) REVERT: E 330 MET cc_start: 0.5771 (tpp) cc_final: 0.5516 (ttt) REVERT: F 21 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: F 68 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: F 138 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7440 (mtp85) REVERT: F 144 THR cc_start: 0.8798 (m) cc_final: 0.8360 (p) REVERT: F 191 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7228 (mp0) REVERT: F 264 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5542 (tt0) outliers start: 36 outliers final: 19 residues processed: 163 average time/residue: 0.5790 time to fit residues: 105.6640 Evaluate side-chains 164 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 264 GLU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 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 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 79 optimal weight: 0.0020 chunk 152 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131150 restraints weight = 17085.299| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.61 r_work: 0.3020 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17448 Z= 0.119 Angle : 0.451 5.710 23958 Z= 0.246 Chirality : 0.044 0.145 2814 Planarity : 0.004 0.042 2848 Dihedral : 10.674 73.503 2996 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 16.39 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 1971 helix: 1.17 (0.24), residues: 509 sheet: 1.60 (0.29), residues: 329 loop : -0.55 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 138 TYR 0.011 0.001 TYR A 342 PHE 0.015 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17448) covalent geometry : angle 0.45145 / 0.25 (23958) hydrogen bonds : bond 0.03670 / 2.42 ( 643) hydrogen bonds : angle 4.87711 / 3.43 ( 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 174 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.653 Fit side-chains REVERT: A 18 GLN cc_start: 0.8778 (mt0) cc_final: 0.8450 (mp10) REVERT: A 188 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: A 199 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8171 (p0) REVERT: A 200 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 204 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8386 (mptp) REVERT: A 215 GLU cc_start: 0.7942 (tt0) cc_final: 0.7428 (tp30) REVERT: A 232 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: B 64 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7905 (mptp) REVERT: B 204 LYS cc_start: 0.8119 (mttp) cc_final: 0.7333 (mmpt) REVERT: B 258 PHE cc_start: 0.7783 (t80) cc_final: 0.7487 (t80) REVERT: B 317 VAL cc_start: 0.7960 (t) cc_final: 0.7757 (p) REVERT: C 149 LYS cc_start: 0.8095 (mttt) cc_final: 0.7671 (mppt) REVERT: C 188 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8022 (tp40) REVERT: C 264 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: D 68 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: D 103 SER cc_start: 0.8022 (p) cc_final: 0.7619 (m) REVERT: D 173 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8085 (tttt) REVERT: E 251 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7578 (tp) REVERT: E 263 PHE cc_start: 0.7845 (p90) cc_final: 0.7604 (p90) REVERT: E 284 GLN cc_start: 0.7242 (tt0) cc_final: 0.6401 (tp40) REVERT: E 330 MET cc_start: 0.5825 (tpp) cc_final: 0.5574 (ttt) REVERT: F 21 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: F 68 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: F 138 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7497 (mtp85) REVERT: F 144 THR cc_start: 0.8813 (m) cc_final: 0.8428 (p) REVERT: F 167 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8398 (pp) REVERT: F 191 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7271 (mp0) REVERT: F 264 GLU cc_start: 0.6566 (mm-30) cc_final: 0.5670 (tt0) outliers start: 41 outliers final: 20 residues processed: 164 average time/residue: 0.5593 time to fit residues: 103.1182 Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 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 167 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 3 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 166 optimal weight: 0.0070 chunk 200 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 40.0000 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132281 restraints weight = 17034.341| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.41 r_work: 0.3039 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0998 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= 0.089 Angle : 0.420 5.591 23958 Z= 0.231 Chirality : 0.042 0.141 2814 Planarity : 0.003 0.040 2848 Dihedral : 10.637 73.496 2996 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.10 % Allowed : 16.56 % 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: 0.49 (0.18), residues: 1971 helix: 1.26 (0.24), residues: 509 sheet: 1.63 (0.29), residues: 326 loop : -0.51 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 138 TYR 0.008 0.001 TYR A 342 PHE 0.010 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (17448) covalent geometry : angle 0.42025 / 0.23 (23958) hydrogen bonds : bond 0.03267 / 2.16 ( 643) hydrogen bonds : angle 4.77627 / 3.37 ( 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 174 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.683 Fit side-chains REVERT: A 18 GLN cc_start: 0.8761 (mt0) cc_final: 0.8439 (mp10) REVERT: A 188 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: A 199 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (p0) REVERT: A 200 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 204 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8391 (mptp) REVERT: A 215 GLU cc_start: 0.7919 (tt0) cc_final: 0.7486 (tp30) REVERT: A 232 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: B 64 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7872 (mptp) REVERT: B 204 LYS cc_start: 0.8115 (mttp) cc_final: 0.7336 (mmpt) REVERT: B 258 PHE cc_start: 0.7767 (t80) cc_final: 0.7478 (t80) REVERT: B 317 VAL cc_start: 0.7946 (t) cc_final: 0.7744 (p) REVERT: C 149 LYS cc_start: 0.8082 (mttt) cc_final: 0.7678 (mppt) REVERT: C 188 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7992 (mm110) REVERT: C 264 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: D 68 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: D 173 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7983 (tttt) REVERT: D 264 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6461 (tt0) REVERT: E 251 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7553 (tp) REVERT: E 263 PHE cc_start: 0.7822 (p90) cc_final: 0.7584 (p90) REVERT: E 284 GLN cc_start: 0.7236 (tt0) cc_final: 0.6407 (tp40) REVERT: E 330 MET cc_start: 0.5835 (tpp) cc_final: 0.5587 (ttt) REVERT: F 21 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: F 68 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: F 138 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7506 (mtp85) REVERT: F 144 THR cc_start: 0.8805 (m) cc_final: 0.8432 (p) REVERT: F 191 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7282 (mp0) REVERT: F 213 PHE cc_start: 0.5910 (t80) cc_final: 0.5659 (t80) REVERT: F 245 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7021 (tt) REVERT: F 264 GLU cc_start: 0.6575 (mm-30) cc_final: 0.5646 (tt0) outliers start: 37 outliers final: 19 residues processed: 165 average time/residue: 0.5638 time to fit residues: 104.2035 Evaluate side-chains 167 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE 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 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 188 GLN 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 189 LEU Chi-restraints excluded: chain E residue 245 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 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 163 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132153 restraints weight = 16931.069| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.49 r_work: 0.3028 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17448 Z= 0.104 Angle : 0.440 5.571 23958 Z= 0.240 Chirality : 0.043 0.145 2814 Planarity : 0.003 0.041 2848 Dihedral : 10.659 73.525 2996 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.04 % Allowed : 16.62 % 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: 0.45 (0.18), residues: 1971 helix: 1.26 (0.24), residues: 506 sheet: 1.59 (0.29), residues: 329 loop : -0.54 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 138 TYR 0.009 0.001 TYR A 342 PHE 0.013 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 (17448) covalent geometry : angle 0.43959 / 0.24 (23958) hydrogen bonds : bond 0.03498 / 2.31 ( 643) hydrogen bonds : angle 4.82747 / 3.40 ( 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: 36 poor density : 135 time to evaluate : 0.615 Fit side-chains REVERT: A 18 GLN cc_start: 0.8773 (mt0) cc_final: 0.8449 (mp10) REVERT: A 188 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: A 199 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8164 (p0) REVERT: A 200 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 204 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8396 (mptp) REVERT: A 215 GLU cc_start: 0.7937 (tt0) cc_final: 0.7445 (tp30) REVERT: A 232 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: B 64 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7903 (mptp) REVERT: B 200 LEU cc_start: 0.7466 (mt) cc_final: 0.7261 (tp) REVERT: B 204 LYS cc_start: 0.8123 (mttp) cc_final: 0.7339 (mmpt) REVERT: B 258 PHE cc_start: 0.7790 (t80) cc_final: 0.7494 (t80) REVERT: C 149 LYS cc_start: 0.8102 (mttt) cc_final: 0.7684 (mppt) REVERT: C 188 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8007 (mm110) REVERT: C 264 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: D 68 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: D 173 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8033 (tttt) REVERT: D 264 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6460 (tt0) REVERT: E 251 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7576 (tp) REVERT: E 263 PHE cc_start: 0.7833 (p90) cc_final: 0.7602 (p90) REVERT: E 284 GLN cc_start: 0.7242 (tt0) cc_final: 0.6415 (tp40) REVERT: E 330 MET cc_start: 0.5819 (tpp) cc_final: 0.5580 (ttt) REVERT: F 21 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: F 68 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: F 138 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7513 (mtp85) REVERT: F 144 THR cc_start: 0.8813 (m) cc_final: 0.8441 (p) REVERT: F 191 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7277 (mp0) REVERT: F 245 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7041 (tt) REVERT: F 264 GLU cc_start: 0.6575 (mm-30) cc_final: 0.5653 (tt0) outliers start: 36 outliers final: 19 residues processed: 161 average time/residue: 0.6114 time to fit residues: 110.1401 Evaluate side-chains 166 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE 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 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131810 restraints weight = 16937.232| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.40 r_work: 0.3030 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17448 Z= 0.102 Angle : 0.437 5.466 23958 Z= 0.239 Chirality : 0.043 0.143 2814 Planarity : 0.003 0.042 2848 Dihedral : 10.663 73.543 2996 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.04 % Allowed : 16.56 % Favored : 81.40 % 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: 1.21 (0.24), residues: 509 sheet: 1.58 (0.29), residues: 333 loop : -0.52 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 138 TYR 0.010 0.001 TYR A 342 PHE 0.013 0.001 PHE F 268 TRP 0.010 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (17448) covalent geometry : angle 0.43712 / 0.24 (23958) hydrogen bonds : bond 0.03462 / 2.28 ( 643) hydrogen bonds : angle 4.81347 / 3.39 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5829.77 seconds wall clock time: 100 minutes 2.50 seconds (6002.50 seconds total)