Starting phenix.real_space_refine on Fri Jul 3 14:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t56_55572/07_2026/9t56_55572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t56_55572/07_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_55572/07_2026/9t56_55572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t56_55572/07_2026/9t56_55572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t56_55572/07_2026/9t56_55572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t56_55572/07_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-6108/lib/python3.11/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: 2.78, per 1000 atoms: 0.20 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: 1.05 Conformation dependent library (CDL) restraints added in 379.2 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: 1.39 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: 1.93 Time building geometry restraints manager: 1.38 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=" C1' DT J 18 " pdb=" N1 DT J 18 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.55e+00 ... (remaining 14912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 20056 1.38 - 2.76: 776 2.76 - 4.14: 200 4.14 - 5.52: 22 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=" N3 DT I 23 " pdb=" C4 DT I 23 " pdb=" O4 DT I 23 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 20 " pdb=" C4 DT I 20 " pdb=" O4 DT I 20 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+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: 1905 0.042 - 0.085: 338 0.085 - 0.127: 97 0.127 - 0.170: 71 0.170 - 0.212: 22 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=" C3' DG G 28 " pdb=" C4' DG G 28 " pdb=" O3' DG G 28 " pdb=" C2' DG G 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" C3' DA I 24 " pdb=" C4' DA I 24 " pdb=" O3' DA I 24 " pdb=" C2' DA I 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.92e-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: 4.340 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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= 0.391 Angle : 0.657 6.904 21058 Z= 0.502 Chirality : 0.046 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/Z covalent geometry : bond 0.00514 / 0.39 (14917) covalent geometry : angle 0.65665 / 0.50 (21058) hydrogen bonds : bond 0.10992 / 7.68 ( 890) hydrogen bonds : angle 5.39992 / 4.02 ( 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 : 0.376 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: 0.5140 time to fit residues: 58.2617 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 : 0.391 ------------------------------------------------------------------------------- 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: 3.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059164 restraints weight = 40881.423| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.46 r_work: 0.2876 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14917 Z= 0.195 Angle : 0.554 8.138 21058 Z= 0.323 Chirality : 0.039 0.186 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.089 174.544 4252 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.63 % Allowed : 24.12 % Favored : 72.25 % 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: 2.79 (0.24), residues: 1241 helix: 2.61 (0.18), residues: 801 sheet: -0.13 (0.46), residues: 134 loop : 0.81 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 156 TYR 0.016 0.002 TYR A 215 PHE 0.011 0.002 PHE A 112 TRP 0.010 0.001 TRP A 121 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (14917) covalent geometry : angle 0.55419 / 0.32 (21058) hydrogen bonds : bond 0.05180 / 3.50 ( 890) hydrogen bonds : angle 4.44236 / 3.33 ( 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 119 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: A 58 CYS cc_start: 0.9052 (OUTLIER) cc_final: 0.7986 (m) REVERT: A 63 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8420 (t) REVERT: A 66 MET cc_start: 0.9135 (pmt) cc_final: 0.8729 (pmt) REVERT: A 139 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8572 (mm-40) REVERT: A 143 ASP cc_start: 0.8856 (m-30) cc_final: 0.8511 (m-30) REVERT: A 191 MET cc_start: 0.9040 (mmt) cc_final: 0.8732 (mmt) REVERT: B 66 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8832 (pmt) REVERT: B 128 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 66 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9064 (pmt) REVERT: C 139 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8329 (mm-40) REVERT: C 188 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8818 (t0) REVERT: C 304 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8233 (mm-40) REVERT: D 139 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8559 (mm-40) REVERT: D 143 ASP cc_start: 0.8936 (m-30) cc_final: 0.8378 (m-30) outliers start: 37 outliers final: 11 residues processed: 108 average time/residue: 0.4741 time to fit residues: 56.6162 Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 64 THR 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 66 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 63 SER 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 258 SER Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 68 ASP 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: 0.8980 chunk 107 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.080953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059429 restraints weight = 40922.632| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.46 r_work: 0.2889 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14917 Z= 0.180 Angle : 0.519 7.694 21058 Z= 0.303 Chirality : 0.037 0.183 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.127 176.311 4225 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.82 % Allowed : 24.51 % Favored : 71.67 % 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: 2.87 (0.24), residues: 1241 helix: 2.62 (0.18), residues: 806 sheet: 0.03 (0.44), residues: 140 loop : 0.93 (0.40), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.019 0.002 TYR B 215 PHE 0.011 0.002 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (14917) covalent geometry : angle 0.51888 / 0.30 (21058) hydrogen bonds : bond 0.04701 / 3.19 ( 890) hydrogen bonds : angle 4.21573 / 3.17 ( 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: 39 poor density : 83 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8896 (pm20) REVERT: A 58 CYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8046 (m) REVERT: A 63 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8368 (t) REVERT: A 66 MET cc_start: 0.9215 (pmt) cc_final: 0.8800 (pmt) REVERT: A 139 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8520 (mm-40) REVERT: A 143 ASP cc_start: 0.8889 (m-30) cc_final: 0.8473 (m-30) REVERT: A 261 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8895 (ptm160) REVERT: B 66 MET cc_start: 0.9170 (pmt) cc_final: 0.8687 (pmt) REVERT: C 58 CYS cc_start: 0.9017 (m) cc_final: 0.8556 (m) REVERT: C 139 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8410 (mm-40) REVERT: C 188 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8827 (t0) REVERT: C 281 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8576 (tmm160) REVERT: C 284 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (mm) REVERT: D 66 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9021 (pmt) REVERT: D 139 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8551 (mm-40) REVERT: D 143 ASP cc_start: 0.8974 (m-30) cc_final: 0.8539 (m-30) outliers start: 39 outliers final: 13 residues processed: 115 average time/residue: 0.5099 time to fit residues: 64.5426 Evaluate side-chains 96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 113 CYS 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 94 SER Chi-restraints excluded: chain B residue 268 MET 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 188 ASP 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 66 MET Chi-restraints excluded: chain D residue 68 ASP 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: 20.0000 chunk 18 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 130 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3557 r_free = 0.3557 target = 0.080924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059477 restraints weight = 40519.901| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.45 r_work: 0.2891 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14917 Z= 0.174 Angle : 0.514 7.565 21058 Z= 0.299 Chirality : 0.037 0.177 2433 Planarity : 0.004 0.043 1959 Dihedral : 23.124 176.100 4218 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.53 % Allowed : 24.61 % Favored : 71.86 % 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: 2.86 (0.24), residues: 1241 helix: 2.59 (0.18), residues: 806 sheet: 0.08 (0.44), residues: 140 loop : 0.95 (0.41), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 23 TYR 0.017 0.002 TYR D 215 PHE 0.011 0.001 PHE C 112 TRP 0.009 0.001 TRP A 121 HIS 0.007 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (14917) covalent geometry : angle 0.51393 / 0.30 (21058) hydrogen bonds : bond 0.04510 / 3.07 ( 890) hydrogen bonds : angle 4.14271 / 3.11 ( 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 114 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8901 (pm20) REVERT: A 58 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8117 (m) REVERT: A 66 MET cc_start: 0.9250 (pmt) cc_final: 0.8815 (pmt) REVERT: A 139 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8525 (mm-40) REVERT: A 143 ASP cc_start: 0.8900 (m-30) cc_final: 0.8491 (m-30) REVERT: A 261 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8878 (ptm160) REVERT: B 66 MET cc_start: 0.9191 (pmt) cc_final: 0.8647 (pmt) REVERT: B 143 ASP cc_start: 0.8780 (m-30) cc_final: 0.8577 (m-30) REVERT: C 58 CYS cc_start: 0.9047 (m) cc_final: 0.8570 (m) REVERT: C 139 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8395 (mm-40) REVERT: C 188 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8821 (m-30) REVERT: C 227 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8146 (mm110) REVERT: C 284 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8694 (mm) REVERT: D 139 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8557 (mm-40) REVERT: D 143 ASP cc_start: 0.9007 (m-30) cc_final: 0.8586 (m-30) outliers start: 36 outliers final: 13 residues processed: 107 average time/residue: 0.5079 time to fit residues: 59.8002 Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 59 MET 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 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 268 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 SER 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: 5.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3517 r_free = 0.3517 target = 0.079102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057468 restraints weight = 41212.901| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.53 r_work: 0.2832 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14917 Z= 0.330 Angle : 0.614 7.262 21058 Z= 0.344 Chirality : 0.041 0.170 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.148 176.537 4214 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.73 % Allowed : 25.00 % 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: 2.60 (0.24), residues: 1241 helix: 2.36 (0.18), residues: 810 sheet: 0.19 (0.46), residues: 134 loop : 0.82 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 51 TYR 0.017 0.002 TYR D 215 PHE 0.015 0.002 PHE C 112 TRP 0.010 0.002 TRP B 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.33 (14917) covalent geometry : angle 0.61355 / 0.34 (21058) hydrogen bonds : bond 0.05522 / 3.76 ( 890) hydrogen bonds : angle 4.27682 / 3.21 ( 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 112 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7859 (pmm-80) REVERT: A 42 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: A 58 CYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8269 (m) REVERT: A 66 MET cc_start: 0.9272 (pmt) cc_final: 0.8855 (pmt) REVERT: A 89 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8518 (tptp) REVERT: A 108 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8822 (ttm) REVERT: A 139 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8575 (mm-40) REVERT: A 143 ASP cc_start: 0.8934 (m-30) cc_final: 0.8585 (m-30) REVERT: A 261 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8910 (ptm160) REVERT: C 58 CYS cc_start: 0.9058 (m) cc_final: 0.8594 (m) REVERT: C 139 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8444 (mm-40) REVERT: C 281 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (tmm160) REVERT: C 284 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8719 (mm) REVERT: D 139 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8496 (mm-40) REVERT: D 143 ASP cc_start: 0.9027 (m-30) cc_final: 0.8549 (m-30) outliers start: 38 outliers final: 16 residues processed: 105 average time/residue: 0.5445 time to fit residues: 62.3809 Evaluate side-chains 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 69 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 63 SER 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 258 SER Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 181 ILE 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: 2.9990 chunk 116 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3569 r_free = 0.3569 target = 0.081557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060131 restraints weight = 40470.314| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.44 r_work: 0.2905 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14917 Z= 0.135 Angle : 0.512 7.051 21058 Z= 0.297 Chirality : 0.036 0.169 2433 Planarity : 0.005 0.049 1959 Dihedral : 23.147 175.458 4211 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.43 % Allowed : 25.29 % 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: 2.77 (0.25), residues: 1241 helix: 2.51 (0.18), residues: 808 sheet: 0.10 (0.46), residues: 136 loop : 0.94 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 51 TYR 0.014 0.002 TYR D 215 PHE 0.009 0.001 PHE C 112 TRP 0.010 0.001 TRP A 121 HIS 0.006 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (14917) covalent geometry : angle 0.51176 / 0.30 (21058) hydrogen bonds : bond 0.04253 / 2.90 ( 890) hydrogen bonds : angle 4.11635 / 3.10 ( 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 118 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7861 (pmm-80) REVERT: A 42 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8900 (pm20) REVERT: A 58 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 66 MET cc_start: 0.9242 (pmt) cc_final: 0.8791 (pmt) REVERT: A 89 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8398 (tptp) REVERT: A 139 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8495 (mm-40) REVERT: A 143 ASP cc_start: 0.8909 (m-30) cc_final: 0.8493 (m-30) REVERT: A 261 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8873 (ptm160) REVERT: B 265 MET cc_start: 0.8538 (tpp) cc_final: 0.7938 (mmm) REVERT: C 58 CYS cc_start: 0.9038 (m) cc_final: 0.8516 (m) REVERT: C 139 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8400 (mm-40) REVERT: C 188 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8801 (t0) REVERT: C 281 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8565 (tmm160) REVERT: C 284 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8646 (mm) REVERT: D 139 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8504 (mm-40) REVERT: D 143 ASP cc_start: 0.8991 (m-30) cc_final: 0.8552 (m-30) outliers start: 35 outliers final: 11 residues processed: 113 average time/residue: 0.5338 time to fit residues: 66.0964 Evaluate side-chains 96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 13 SER Chi-restraints excluded: chain B residue 94 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 188 ASP 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 68 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 24 optimal weight: 0.0570 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS A 93 GLN ** B 84 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.081734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060379 restraints weight = 40445.980| |-----------------------------------------------------------------------------| r_work (start): 0.3087 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: 0.8627 moved from start: 0.1382 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= 0.139 Angle : 0.515 8.697 21058 Z= 0.296 Chirality : 0.036 0.162 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.098 176.509 4211 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.75 % Allowed : 25.78 % Favored : 71.47 % 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: 2.83 (0.25), residues: 1241 helix: 2.55 (0.18), residues: 808 sheet: 0.24 (0.45), residues: 138 loop : 0.91 (0.41), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 51 TYR 0.019 0.001 TYR A 307 PHE 0.010 0.001 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (14917) covalent geometry : angle 0.51511 / 0.30 (21058) hydrogen bonds : bond 0.04167 / 2.84 ( 890) hydrogen bonds : angle 4.06279 / 3.06 ( 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 109 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: A 58 CYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8138 (m) REVERT: A 66 MET cc_start: 0.9217 (pmt) cc_final: 0.8750 (pmt) REVERT: A 89 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8387 (tptp) REVERT: A 139 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8501 (mm-40) REVERT: A 143 ASP cc_start: 0.8920 (m-30) cc_final: 0.8575 (m-30) REVERT: B 265 MET cc_start: 0.8606 (tpp) cc_final: 0.7968 (mmm) REVERT: C 58 CYS cc_start: 0.9033 (m) cc_final: 0.8553 (m) REVERT: C 139 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8417 (mm-40) REVERT: C 188 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8792 (t0) REVERT: C 281 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8578 (tmm160) REVERT: C 284 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8684 (mm) REVERT: D 139 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8482 (mm-40) REVERT: D 143 ASP cc_start: 0.9004 (m-30) cc_final: 0.8562 (m-30) outliers start: 28 outliers final: 12 residues processed: 107 average time/residue: 0.5149 time to fit residues: 60.4609 Evaluate side-chains 95 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 89 LYS 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 269 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 68 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3566 r_free = 0.3566 target = 0.081342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060009 restraints weight = 40539.191| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.44 r_work: 0.2905 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14917 Z= 0.162 Angle : 0.512 8.060 21058 Z= 0.294 Chirality : 0.037 0.156 2433 Planarity : 0.004 0.041 1959 Dihedral : 23.069 176.986 4210 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.65 % Allowed : 26.08 % 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: 2.84 (0.25), residues: 1241 helix: 2.56 (0.18), residues: 808 sheet: 0.20 (0.44), residues: 138 loop : 0.90 (0.41), residues: 295 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 0.010 0.001 PHE A 112 TRP 0.009 0.001 TRP A 121 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14917) covalent geometry : angle 0.51225 / 0.29 (21058) hydrogen bonds : bond 0.04247 / 2.90 ( 890) hydrogen bonds : angle 4.03797 / 3.05 ( 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 107 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7857 (pmm-80) REVERT: A 42 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8900 (pm20) REVERT: A 58 CYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8153 (m) REVERT: A 66 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8754 (pmt) REVERT: A 89 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8435 (tptp) REVERT: A 139 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8520 (mm-40) REVERT: A 143 ASP cc_start: 0.8917 (m-30) cc_final: 0.8573 (m-30) REVERT: B 66 MET cc_start: 0.9105 (pmt) cc_final: 0.8546 (pmt) REVERT: C 58 CYS cc_start: 0.9040 (m) cc_final: 0.8589 (m) REVERT: C 188 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (t0) REVERT: C 281 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8589 (tmm160) REVERT: C 284 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8678 (mm) REVERT: D 45 ARG cc_start: 0.8995 (ttp-110) cc_final: 0.8603 (ttm110) outliers start: 27 outliers final: 10 residues processed: 102 average time/residue: 0.5692 time to fit residues: 63.2973 Evaluate side-chains 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 66 MET 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 94 SER Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 133 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 6 HIS C 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.079812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058304 restraints weight = 40847.812| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.49 r_work: 0.2860 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14917 Z= 0.268 Angle : 0.585 9.939 21058 Z= 0.329 Chirality : 0.040 0.203 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.082 177.335 4210 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.55 % Allowed : 26.27 % Favored : 71.18 % 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: 2.66 (0.24), residues: 1241 helix: 2.42 (0.18), residues: 809 sheet: 0.16 (0.44), residues: 138 loop : 0.85 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 51 TYR 0.020 0.002 TYR D 215 PHE 0.014 0.002 PHE C 112 TRP 0.010 0.002 TRP A 46 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.27 (14917) covalent geometry : angle 0.58526 / 0.33 (21058) hydrogen bonds : bond 0.04992 / 3.41 ( 890) hydrogen bonds : angle 4.17434 / 3.15 ( 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 101 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7873 (pmm-80) REVERT: A 42 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8931 (pm20) REVERT: A 58 CYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8226 (m) REVERT: A 66 MET cc_start: 0.9240 (pmt) cc_final: 0.8786 (pmt) REVERT: A 89 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8462 (tptp) REVERT: A 139 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8555 (mm-40) REVERT: A 143 ASP cc_start: 0.8945 (m-30) cc_final: 0.8557 (m-30) REVERT: A 261 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8910 (ptm160) REVERT: B 139 GLN cc_start: 0.9251 (tt0) cc_final: 0.8675 (tm-30) REVERT: B 143 ASP cc_start: 0.9048 (m-30) cc_final: 0.8577 (m-30) REVERT: B 265 MET cc_start: 0.8614 (tpp) cc_final: 0.8152 (mmm) REVERT: B 298 MET cc_start: 0.9580 (tpt) cc_final: 0.8701 (tpt) REVERT: C 58 CYS cc_start: 0.9069 (m) cc_final: 0.8603 (m) REVERT: C 139 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: C 281 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8597 (tmm160) REVERT: C 284 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8670 (mm) REVERT: D 139 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8828 (mm-40) REVERT: D 143 ASP cc_start: 0.9045 (m-30) cc_final: 0.8735 (m-30) outliers start: 26 outliers final: 8 residues processed: 96 average time/residue: 0.6041 time to fit residues: 63.1552 Evaluate side-chains 87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 94 SER Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 68 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 137 optimal weight: 40.0000 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 6 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058896 restraints weight = 40613.587| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.45 r_work: 0.2875 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14917 Z= 0.213 Angle : 0.557 10.122 21058 Z= 0.316 Chirality : 0.038 0.188 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.100 176.598 4210 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.25 % Allowed : 26.37 % 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: 2.65 (0.24), residues: 1241 helix: 2.42 (0.18), residues: 809 sheet: 0.13 (0.44), residues: 138 loop : 0.84 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.006 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (14917) covalent geometry : angle 0.55737 / 0.32 (21058) hydrogen bonds : bond 0.04606 / 3.16 ( 890) hydrogen bonds : angle 4.14731 / 3.14 ( 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 96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7864 (pmm-80) REVERT: A 42 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: A 58 CYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8164 (m) REVERT: A 66 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8760 (pmt) REVERT: A 89 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8430 (tptp) REVERT: A 139 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8541 (mm-40) REVERT: A 143 ASP cc_start: 0.8930 (m-30) cc_final: 0.8528 (m-30) REVERT: A 261 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8890 (ptm160) REVERT: B 139 GLN cc_start: 0.9234 (tt0) cc_final: 0.8709 (tm-30) REVERT: B 143 ASP cc_start: 0.9008 (m-30) cc_final: 0.8271 (m-30) REVERT: B 265 MET cc_start: 0.8642 (tpp) cc_final: 0.8133 (mmm) REVERT: C 58 CYS cc_start: 0.9040 (m) cc_final: 0.8566 (m) REVERT: C 139 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8656 (mm-40) REVERT: C 284 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8662 (mm) outliers start: 23 outliers final: 12 residues processed: 91 average time/residue: 0.5863 time to fit residues: 58.4470 Evaluate side-chains 91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 66 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 LYS 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 94 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 68 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 130 optimal weight: 50.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 6 HIS C 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059211 restraints weight = 40343.892| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.43 r_work: 0.2883 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14917 Z= 0.203 Angle : 0.550 10.092 21058 Z= 0.312 Chirality : 0.038 0.188 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.086 176.809 4210 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.25 % Allowed : 26.47 % 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: 2.68 (0.24), residues: 1241 helix: 2.44 (0.18), residues: 809 sheet: 0.10 (0.44), residues: 138 loop : 0.84 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 51 TYR 0.027 0.002 TYR D 215 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/Z covalent geometry : bond 0.00416 / 0.20 (14917) covalent geometry : angle 0.54956 / 0.31 (21058) hydrogen bonds : bond 0.04487 / 3.07 ( 890) hydrogen bonds : angle 4.12587 / 3.12 ( 2415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.14 seconds wall clock time: 56 minutes 1.78 seconds (3361.78 seconds total)