Starting phenix.real_space_refine on Wed Mar 4 15:16:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t56_55572/03_2026/9t56_55572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t56_55572/03_2026/9t56_55572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t56_55572/03_2026/9t56_55572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t56_55572/03_2026/9t56_55572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t56_55572/03_2026/9t56_55572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t56_55572/03_2026/9t56_55572.map" } resolution = 2.81 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= 0.004 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 P 208 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8170 2.51 5 N 2666 2.21 5 O 3118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14212 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2500 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2426 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2500 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain: "D" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2431 Classifications: {'peptide': 309} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "E" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 23, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 43} Chain: "F" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1442 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 27, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 55} Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 421 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "H" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 438 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "J" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 435 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14212 At special positions: 0 Unit cell: (102.05, 111.8, 110.5, 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) S 48 16.00 P 208 15.00 Mg 2 11.99 O 3118 8.00 N 2666 7.00 C 8170 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: 1.32 Conformation dependent library (CDL) restraints added in 377.2 milliseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 68.0% alpha, 10.0% beta 79 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 84 through 96 removed outlier: 3.674A pdb=" N GLY A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.637A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 187 Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.875A pdb=" N ILE A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 256 through 274 removed outlier: 4.588A pdb=" N MET A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Proline residue: A 266 - end of helix removed outlier: 3.561A pdb=" N THR A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.634A pdb=" N ASN A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 65 through 76 removed outlier: 4.705A pdb=" N VAL B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.644A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.631A pdb=" N ASP B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.809A pdb=" N ILE B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 256 through 274 removed outlier: 4.593A pdb=" N MET B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Proline residue: B 266 - end of helix Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 96 removed outlier: 3.531A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 125 through 155 removed outlier: 3.917A pdb=" N THR C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 188 removed outlier: 4.749A pdb=" N SER C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.701A pdb=" N ILE C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 256 through 274 removed outlier: 4.475A pdb=" N MET C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 64 through 76 removed outlier: 4.214A pdb=" N ASP D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 101 through 117 Processing helix chain 'D' and resid 125 through 155 removed outlier: 4.154A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.684A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 256 through 274 removed outlier: 4.387A pdb=" N MET D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Proline residue: D 266 - end of helix Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.784A pdb=" N ASN D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.475A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 241 removed outlier: 5.947A pdb=" N ARG A 237 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A 249 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR A 239 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 34 removed outlier: 3.537A pdb=" N ASP B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 60 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.400A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 237 removed outlier: 3.606A pdb=" N ARG C 250 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA8, first strand: chain 'D' and resid 28 through 34 removed outlier: 3.707A pdb=" N LEU D 22 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 7 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.581A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 202 hydrogen bonds 396 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2099 1.32 - 1.44: 4905 1.44 - 1.57: 7419 1.57 - 1.69: 406 1.69 - 1.81: 88 Bond restraints: 14917 Sorted by residual: bond pdb=" CA SER B 258 " pdb=" CB SER B 258 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.53e+01 bond pdb=" CA SER A 63 " pdb=" CB SER A 63 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.23e+01 bond pdb=" CA SER D 63 " pdb=" CB SER D 63 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.04e+01 bond pdb=" C ALA B 254 " pdb=" O ALA B 254 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.17e-02 7.31e+03 9.94e+00 bond pdb=" CA ALA A 61 " pdb=" CB ALA A 61 " ideal model delta sigma weight residual 1.527 1.489 0.037 1.27e-02 6.20e+03 8.55e+00 ... (remaining 14912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 20253 1.38 - 2.76: 645 2.76 - 4.14: 135 4.14 - 5.52: 21 5.52 - 6.90: 4 Bond angle restraints: 21058 Sorted by residual: angle pdb=" N ALA D 70 " pdb=" CA ALA D 70 " pdb=" C ALA D 70 " ideal model delta sigma weight residual 110.97 105.91 5.06 1.09e+00 8.42e-01 2.15e+01 angle pdb=" N GLU D 60 " pdb=" CA GLU D 60 " pdb=" C GLU D 60 " ideal model delta sigma weight residual 110.50 104.14 6.36 1.41e+00 5.03e-01 2.04e+01 angle pdb=" C SER C 63 " pdb=" CA SER C 63 " pdb=" CB SER C 63 " ideal model delta sigma weight residual 116.54 111.37 5.17 1.15e+00 7.56e-01 2.02e+01 angle pdb=" N THR A 64 " pdb=" CA THR A 64 " pdb=" C THR A 64 " ideal model delta sigma weight residual 112.88 107.64 5.24 1.29e+00 6.01e-01 1.65e+01 angle pdb=" C THR D 62 " pdb=" CA THR D 62 " pdb=" CB THR D 62 " ideal model delta sigma weight residual 112.09 117.83 -5.74 1.43e+00 4.89e-01 1.61e+01 ... (remaining 21053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 8118 35.26 - 70.52: 810 70.52 - 105.78: 66 105.78 - 141.04: 2 141.04 - 176.30: 3 Dihedral angle restraints: 8999 sinusoidal: 5380 harmonic: 3619 Sorted by residual: dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual -128.00 48.30 -176.30 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 161 " pdb=" C1' U F 161 " pdb=" N1 U F 161 " pdb=" C2 U F 161 " ideal model delta sinusoidal sigma weight residual -128.00 31.38 -159.38 1 1.70e+01 3.46e-03 6.43e+01 dihedral pdb=" C4' U F 175 " pdb=" C3' U F 175 " pdb=" O3' U F 175 " pdb=" P C F 176 " ideal model delta sinusoidal sigma weight residual 220.00 72.32 147.68 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 8996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1904 0.042 - 0.085: 387 0.085 - 0.127: 127 0.127 - 0.170: 13 0.170 - 0.212: 2 Chirality restraints: 2433 Sorted by residual: chirality pdb=" CA MET D 59 " pdb=" N MET D 59 " pdb=" C MET D 59 " pdb=" CB MET D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA MET A 66 " pdb=" N MET A 66 " pdb=" C MET A 66 " pdb=" CB MET A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C1' C E 48 " pdb=" O4' C E 48 " pdb=" C2' C E 48 " pdb=" N1 C E 48 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2430 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 254 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA B 254 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA B 254 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY B 255 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 46 " 0.027 2.00e-02 2.50e+03 1.20e-02 4.33e+00 pdb=" N9 G E 46 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G E 46 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G E 46 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G E 46 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G E 46 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G E 46 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G E 46 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G E 46 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G E 46 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G E 46 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G E 46 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G F 168 " 0.027 2.00e-02 2.50e+03 1.18e-02 4.20e+00 pdb=" N9 G F 168 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G F 168 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G F 168 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G F 168 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G F 168 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G F 168 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G F 168 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G F 168 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G F 168 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G F 168 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G F 168 " -0.002 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 1 1.79 - 2.57: 65 2.57 - 3.34: 18303 3.34 - 4.12: 39988 4.12 - 4.90: 67569 Nonbonded interactions: 125926 Sorted by model distance: nonbonded pdb=" OE2 GLU D 60 " pdb="MG MG I 101 " model vdw 1.011 2.170 nonbonded pdb=" OP1 DA G 26 " pdb="MG MG G 101 " model vdw 1.814 2.170 nonbonded pdb=" O3' DT G 25 " pdb="MG MG G 101 " model vdw 1.834 2.170 nonbonded pdb=" OP1 DT I 21 " pdb="MG MG I 101 " model vdw 1.850 2.170 nonbonded pdb=" O3' DT I 20 " pdb="MG MG I 101 " model vdw 1.981 2.170 ... (remaining 125921 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 4 through 238 or resid 249 through 321)) selection = chain 'B' selection = (chain 'C' and (resid 4 through 238 or resid 249 through 321)) selection = (chain 'D' and (resid 4 through 238 or resid 249 through 321)) } 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.005 0.061 14917 Z= 0.255 Angle : 0.610 6.904 21058 Z= 0.367 Chirality : 0.040 0.212 2433 Planarity : 0.004 0.041 1959 Dihedral : 22.626 176.299 6649 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.65 % Allowed : 25.78 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.24), residues: 1241 helix: 2.58 (0.18), residues: 794 sheet: -0.39 (0.44), residues: 138 loop : 0.75 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 156 TYR 0.013 0.002 TYR D 215 PHE 0.010 0.001 PHE C 112 TRP 0.007 0.001 TRP A 121 HIS 0.010 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00470 (14917) covalent geometry : angle 0.61008 (21058) hydrogen bonds : bond 0.10992 ( 890) hydrogen bonds : angle 5.39992 ( 2415) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 CYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7768 (m) REVERT: A 63 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8337 (t) REVERT: A 66 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8642 (pmt) REVERT: A 139 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8697 (mm-40) REVERT: B 128 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 139 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7953 (tm-30) REVERT: C 188 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8813 (t0) REVERT: D 59 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8806 (mtm) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.5974 time to fit residues: 67.3615 Evaluate side-chains 98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 68 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.081148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.059767 restraints weight = 41174.118| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.45 r_work: 0.2904 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14917 Z= 0.173 Angle : 0.547 7.874 21058 Z= 0.296 Chirality : 0.036 0.188 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.006 174.659 4252 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.24 % Allowed : 23.73 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.25), residues: 1241 helix: 2.76 (0.18), residues: 805 sheet: -0.39 (0.44), residues: 138 loop : 0.95 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 156 TYR 0.013 0.002 TYR A 215 PHE 0.011 0.001 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.009 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00368 (14917) covalent geometry : angle 0.54695 (21058) hydrogen bonds : bond 0.04323 ( 890) hydrogen bonds : angle 4.23164 ( 2415) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8898 (pm20) REVERT: A 58 CYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8048 (m) REVERT: A 66 MET cc_start: 0.9244 (pmt) cc_final: 0.8850 (pmt) REVERT: A 139 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8557 (mm-40) REVERT: A 143 ASP cc_start: 0.8863 (m-30) cc_final: 0.8531 (m-30) REVERT: B 66 MET cc_start: 0.9202 (pmt) cc_final: 0.8936 (pmt) REVERT: B 128 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 58 CYS cc_start: 0.9057 (m) cc_final: 0.8662 (m) REVERT: C 66 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.9134 (pmt) REVERT: C 139 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8147 (tm-30) REVERT: C 187 ASP cc_start: 0.9014 (t0) cc_final: 0.8800 (t0) REVERT: C 188 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8782 (t0) REVERT: C 284 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 66 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8861 (pmt) outliers start: 33 outliers final: 7 residues processed: 110 average time/residue: 0.5743 time to fit residues: 69.2549 Evaluate side-chains 91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 0.0270 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059823 restraints weight = 40882.802| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.46 r_work: 0.2901 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14917 Z= 0.177 Angle : 0.528 6.758 21058 Z= 0.287 Chirality : 0.036 0.160 2433 Planarity : 0.005 0.040 1959 Dihedral : 22.979 175.423 4217 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.63 % Allowed : 24.22 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.24), residues: 1241 helix: 2.69 (0.18), residues: 809 sheet: -0.06 (0.45), residues: 134 loop : 0.85 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 156 TYR 0.016 0.002 TYR A 307 PHE 0.011 0.001 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.007 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00377 (14917) covalent geometry : angle 0.52794 (21058) hydrogen bonds : bond 0.04188 ( 890) hydrogen bonds : angle 4.12718 ( 2415) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8906 (pm20) REVERT: A 58 CYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8140 (m) REVERT: A 63 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8421 (t) REVERT: A 66 MET cc_start: 0.9263 (pmt) cc_final: 0.8760 (pmt) REVERT: A 108 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8908 (ttm) REVERT: A 139 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8808 (mm-40) REVERT: B 66 MET cc_start: 0.9219 (pmt) cc_final: 0.8585 (pmt) REVERT: B 128 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 139 GLN cc_start: 0.9286 (tt0) cc_final: 0.9077 (tt0) REVERT: C 58 CYS cc_start: 0.9049 (m) cc_final: 0.8592 (m) REVERT: C 139 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8419 (mm-40) REVERT: C 187 ASP cc_start: 0.9084 (t0) cc_final: 0.8849 (t0) REVERT: C 188 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8796 (t0) REVERT: D 139 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8667 (mm-40) REVERT: D 143 ASP cc_start: 0.8982 (m-30) cc_final: 0.8593 (m-30) outliers start: 37 outliers final: 13 residues processed: 114 average time/residue: 0.5782 time to fit residues: 72.0400 Evaluate side-chains 96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.080526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059184 restraints weight = 41033.571| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.44 r_work: 0.2888 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14917 Z= 0.204 Angle : 0.537 5.641 21058 Z= 0.291 Chirality : 0.036 0.153 2433 Planarity : 0.005 0.045 1959 Dihedral : 22.979 174.656 4211 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.02 % Allowed : 23.33 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.24), residues: 1241 helix: 2.60 (0.18), residues: 811 sheet: 0.02 (0.45), residues: 136 loop : 0.87 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.016 0.002 TYR A 307 PHE 0.011 0.002 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.006 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00435 (14917) covalent geometry : angle 0.53670 (21058) hydrogen bonds : bond 0.04285 ( 890) hydrogen bonds : angle 4.08642 ( 2415) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7843 (pmm-80) REVERT: A 42 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8897 (pm20) REVERT: A 63 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8474 (t) REVERT: A 139 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8548 (mm-40) REVERT: A 143 ASP cc_start: 0.8908 (m-30) cc_final: 0.8517 (m-30) REVERT: A 261 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8920 (ptm160) REVERT: B 128 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 265 MET cc_start: 0.8642 (tpp) cc_final: 0.8083 (mmm) REVERT: C 58 CYS cc_start: 0.9045 (m) cc_final: 0.8630 (m) REVERT: C 187 ASP cc_start: 0.9077 (t0) cc_final: 0.8825 (t0) REVERT: C 281 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (tmm160) REVERT: C 284 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8749 (mm) REVERT: D 144 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8999 (mtt) outliers start: 41 outliers final: 12 residues processed: 117 average time/residue: 0.6693 time to fit residues: 84.8631 Evaluate side-chains 97 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059208 restraints weight = 40977.826| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.46 r_work: 0.2883 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14917 Z= 0.204 Angle : 0.544 7.279 21058 Z= 0.294 Chirality : 0.036 0.152 2433 Planarity : 0.005 0.041 1959 Dihedral : 22.983 174.608 4207 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.24 % Allowed : 24.12 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.24), residues: 1241 helix: 2.60 (0.18), residues: 811 sheet: 0.07 (0.46), residues: 136 loop : 0.83 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 51 TYR 0.017 0.002 TYR A 307 PHE 0.011 0.002 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00436 (14917) covalent geometry : angle 0.54370 (21058) hydrogen bonds : bond 0.04229 ( 890) hydrogen bonds : angle 4.06669 ( 2415) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7864 (pmm-80) REVERT: A 42 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: A 63 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 89 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8447 (tptp) REVERT: A 139 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8516 (mm-40) REVERT: A 143 ASP cc_start: 0.8910 (m-30) cc_final: 0.8509 (m-30) REVERT: A 261 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8915 (ptm160) REVERT: B 128 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 58 CYS cc_start: 0.9040 (m) cc_final: 0.8596 (m) REVERT: C 139 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8265 (tm-30) REVERT: C 187 ASP cc_start: 0.9106 (t0) cc_final: 0.8846 (t0) REVERT: C 258 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (t) REVERT: C 281 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8590 (tmm160) REVERT: C 284 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8677 (mm) REVERT: D 45 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8632 (ttm110) outliers start: 33 outliers final: 12 residues processed: 111 average time/residue: 0.6044 time to fit residues: 73.3629 Evaluate side-chains 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 44 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060382 restraints weight = 40498.340| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.44 r_work: 0.2915 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14917 Z= 0.153 Angle : 0.518 6.543 21058 Z= 0.280 Chirality : 0.035 0.150 2433 Planarity : 0.004 0.041 1959 Dihedral : 22.955 174.911 4207 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.04 % Allowed : 24.80 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.25), residues: 1241 helix: 2.69 (0.18), residues: 809 sheet: 0.18 (0.45), residues: 140 loop : 0.87 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.018 0.001 TYR A 307 PHE 0.010 0.001 PHE A 112 TRP 0.008 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00326 (14917) covalent geometry : angle 0.51766 (21058) hydrogen bonds : bond 0.03885 ( 890) hydrogen bonds : angle 3.98343 ( 2415) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7844 (pmm-80) REVERT: A 42 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8899 (pm20) REVERT: A 58 CYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8343 (m) REVERT: A 89 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8387 (tptp) REVERT: A 108 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8782 (ttm) REVERT: A 139 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8512 (mm-40) REVERT: A 143 ASP cc_start: 0.8916 (m-30) cc_final: 0.8570 (m-30) REVERT: B 265 MET cc_start: 0.8484 (tpp) cc_final: 0.7970 (mmm) REVERT: B 298 MET cc_start: 0.9513 (tpt) cc_final: 0.8611 (tpt) REVERT: C 58 CYS cc_start: 0.9002 (m) cc_final: 0.8584 (m) REVERT: C 139 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8275 (tm-30) REVERT: C 187 ASP cc_start: 0.9093 (t0) cc_final: 0.8826 (t0) REVERT: C 258 SER cc_start: 0.9127 (OUTLIER) cc_final: 0.8865 (t) REVERT: C 281 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8592 (tmm160) REVERT: C 284 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8661 (mm) REVERT: D 45 ARG cc_start: 0.8992 (ttp-110) cc_final: 0.8634 (ttm110) REVERT: D 139 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8697 (mm-40) REVERT: D 143 ASP cc_start: 0.8924 (m-30) cc_final: 0.8478 (m-30) outliers start: 31 outliers final: 14 residues processed: 112 average time/residue: 0.6106 time to fit residues: 74.5526 Evaluate side-chains 101 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 259 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060729 restraints weight = 40864.955| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.44 r_work: 0.2935 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14917 Z= 0.148 Angle : 0.513 7.019 21058 Z= 0.277 Chirality : 0.034 0.149 2433 Planarity : 0.004 0.046 1959 Dihedral : 22.877 176.071 4207 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.84 % Allowed : 24.71 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.25), residues: 1241 helix: 2.74 (0.18), residues: 809 sheet: 0.19 (0.45), residues: 140 loop : 0.85 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.017 0.001 TYR A 307 PHE 0.010 0.001 PHE A 112 TRP 0.008 0.001 TRP A 121 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00315 (14917) covalent geometry : angle 0.51278 (21058) hydrogen bonds : bond 0.03800 ( 890) hydrogen bonds : angle 3.95620 ( 2415) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8896 (pm20) REVERT: A 58 CYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8333 (m) REVERT: A 66 MET cc_start: 0.9249 (pmt) cc_final: 0.8763 (pmt) REVERT: A 108 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8794 (ttm) REVERT: A 139 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8583 (mm-40) REVERT: A 143 ASP cc_start: 0.8932 (m-30) cc_final: 0.8648 (m-30) REVERT: B 58 CYS cc_start: 0.8640 (m) cc_final: 0.8282 (t) REVERT: B 139 GLN cc_start: 0.9182 (tt0) cc_final: 0.8795 (tm-30) REVERT: B 143 ASP cc_start: 0.8923 (m-30) cc_final: 0.8299 (m-30) REVERT: B 265 MET cc_start: 0.8523 (tpp) cc_final: 0.7950 (mmm) REVERT: C 58 CYS cc_start: 0.8984 (m) cc_final: 0.8581 (m) REVERT: C 139 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8497 (mm-40) REVERT: C 187 ASP cc_start: 0.9062 (t0) cc_final: 0.8794 (t0) REVERT: C 258 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8844 (t) REVERT: C 281 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8640 (tmm160) REVERT: D 45 ARG cc_start: 0.8990 (ttp-110) cc_final: 0.8625 (ttm110) REVERT: D 139 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8634 (mm-40) REVERT: D 143 ASP cc_start: 0.8903 (m-30) cc_final: 0.8460 (m-30) REVERT: D 153 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8504 (tm-30) outliers start: 29 outliers final: 18 residues processed: 110 average time/residue: 0.5806 time to fit residues: 69.7594 Evaluate side-chains 99 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.058914 restraints weight = 40778.071| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.48 r_work: 0.2862 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14917 Z= 0.247 Angle : 0.566 7.141 21058 Z= 0.304 Chirality : 0.037 0.152 2433 Planarity : 0.005 0.042 1959 Dihedral : 22.900 176.590 4207 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.14 % Allowed : 24.90 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.25), residues: 1241 helix: 2.57 (0.18), residues: 811 sheet: 0.26 (0.45), residues: 138 loop : 0.72 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 51 TYR 0.019 0.002 TYR A 307 PHE 0.012 0.002 PHE C 112 TRP 0.009 0.001 TRP A 46 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00528 (14917) covalent geometry : angle 0.56557 (21058) hydrogen bonds : bond 0.04440 ( 890) hydrogen bonds : angle 4.06717 ( 2415) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7837 (pmm-80) REVERT: A 42 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8946 (pm20) REVERT: A 58 CYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8355 (m) REVERT: A 66 MET cc_start: 0.9246 (pmt) cc_final: 0.8771 (pmt) REVERT: A 89 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8446 (tptp) REVERT: A 108 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8788 (ttm) REVERT: A 139 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8552 (mm-40) REVERT: A 143 ASP cc_start: 0.8930 (m-30) cc_final: 0.8529 (m-30) REVERT: A 261 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8916 (ptm160) REVERT: C 58 CYS cc_start: 0.9042 (m) cc_final: 0.8572 (m) REVERT: C 139 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8588 (mm-40) REVERT: C 187 ASP cc_start: 0.9127 (t0) cc_final: 0.8860 (t0) REVERT: C 258 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8947 (t) REVERT: C 281 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8579 (tmm160) REVERT: D 45 ARG cc_start: 0.9004 (ttp-110) cc_final: 0.8611 (ttm110) REVERT: D 153 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8553 (tm-30) outliers start: 32 outliers final: 16 residues processed: 103 average time/residue: 0.5948 time to fit residues: 66.8850 Evaluate side-chains 97 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.057928 restraints weight = 41405.649| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.45 r_work: 0.2859 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14917 Z= 0.264 Angle : 0.591 7.439 21058 Z= 0.319 Chirality : 0.038 0.194 2433 Planarity : 0.005 0.058 1959 Dihedral : 22.939 176.381 4207 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.33 % Allowed : 24.90 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.24), residues: 1241 helix: 2.42 (0.18), residues: 811 sheet: 0.14 (0.44), residues: 138 loop : 0.71 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 51 TYR 0.018 0.002 TYR A 307 PHE 0.013 0.002 PHE C 112 TRP 0.010 0.001 TRP D 46 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00565 (14917) covalent geometry : angle 0.59052 (21058) hydrogen bonds : bond 0.04678 ( 890) hydrogen bonds : angle 4.17360 ( 2415) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7884 (pmm-80) REVERT: A 42 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: A 58 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 63 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8455 (t) REVERT: A 66 MET cc_start: 0.9297 (pmt) cc_final: 0.8849 (pmt) REVERT: A 89 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8498 (tptp) REVERT: A 108 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8766 (ttm) REVERT: A 139 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8488 (mm-40) REVERT: A 143 ASP cc_start: 0.8931 (m-30) cc_final: 0.8526 (m-30) REVERT: A 261 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8916 (ptm160) REVERT: B 139 GLN cc_start: 0.9203 (tt0) cc_final: 0.8807 (tm-30) REVERT: B 143 ASP cc_start: 0.8941 (m-30) cc_final: 0.8269 (m-30) REVERT: B 265 MET cc_start: 0.8643 (tpp) cc_final: 0.8132 (mmm) REVERT: C 58 CYS cc_start: 0.9039 (m) cc_final: 0.8593 (m) REVERT: C 139 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8686 (mm-40) REVERT: C 187 ASP cc_start: 0.9094 (t0) cc_final: 0.8824 (t0) REVERT: D 45 ARG cc_start: 0.8979 (ttp-110) cc_final: 0.8582 (ttm110) REVERT: D 153 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8615 (tm-30) outliers start: 34 outliers final: 16 residues processed: 105 average time/residue: 0.5952 time to fit residues: 68.3887 Evaluate side-chains 96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN C 6 HIS C 145 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061661 restraints weight = 40714.934| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.42 r_work: 0.2964 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14917 Z= 0.125 Angle : 0.520 9.411 21058 Z= 0.281 Chirality : 0.034 0.160 2433 Planarity : 0.005 0.048 1959 Dihedral : 22.777 178.533 4207 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.76 % Allowed : 26.86 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.25), residues: 1241 helix: 2.72 (0.18), residues: 809 sheet: 0.16 (0.44), residues: 140 loop : 0.72 (0.42), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 51 TYR 0.016 0.002 TYR A 307 PHE 0.012 0.001 PHE C 280 TRP 0.008 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00264 (14917) covalent geometry : angle 0.52037 (21058) hydrogen bonds : bond 0.03711 ( 890) hydrogen bonds : angle 3.97860 ( 2415) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 CYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8221 (m) REVERT: A 66 MET cc_start: 0.9213 (pmt) cc_final: 0.8761 (pmt) REVERT: A 108 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8783 (ttm) REVERT: A 139 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8925 (mm-40) REVERT: A 227 GLN cc_start: 0.8981 (mt0) cc_final: 0.8716 (mt0) REVERT: B 58 CYS cc_start: 0.8563 (m) cc_final: 0.8238 (t) REVERT: B 265 MET cc_start: 0.8480 (tpp) cc_final: 0.7803 (mmm) REVERT: C 58 CYS cc_start: 0.8977 (m) cc_final: 0.8580 (m) REVERT: C 139 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8552 (mm-40) REVERT: C 187 ASP cc_start: 0.9041 (t0) cc_final: 0.8765 (t0) REVERT: D 45 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8613 (ttm110) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.6125 time to fit residues: 69.5550 Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 74 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059984 restraints weight = 40679.856| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.42 r_work: 0.2918 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14917 Z= 0.182 Angle : 0.549 9.096 21058 Z= 0.296 Chirality : 0.036 0.246 2433 Planarity : 0.005 0.044 1959 Dihedral : 22.751 179.101 4207 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.96 % Allowed : 26.76 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.25), residues: 1241 helix: 2.66 (0.18), residues: 809 sheet: 0.16 (0.43), residues: 140 loop : 0.74 (0.42), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 51 TYR 0.018 0.001 TYR A 307 PHE 0.012 0.001 PHE C 280 TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00392 (14917) covalent geometry : angle 0.54875 (21058) hydrogen bonds : bond 0.04089 ( 890) hydrogen bonds : angle 4.03372 ( 2415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.70 seconds wall clock time: 62 minutes 48.71 seconds (3768.71 seconds total)