Starting phenix.real_space_refine on Thu Aug 6 08:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t56_55572/08_2026/9t56_55572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t56_55572/08_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_55572/08_2026/9t56_55572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t56_55572/08_2026/9t56_55572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t56_55572/08_2026/9t56_55572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t56_55572/08_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-2.2rc3-6140/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: 3.32, per 1000 atoms: 0.23 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: 1.20 Conformation dependent library (CDL) restraints added in 495.6 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: 1.89 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: 2.72 Time building geometry restraints manager: 1.59 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: 19730 1.38 - 2.76: 1094 2.76 - 4.14: 208 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: 1795 0.042 - 0.085: 324 0.085 - 0.127: 219 0.127 - 0.170: 73 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.360 Find NCS groups from input model: 0.220 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:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- 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= 0.399 Angle : 0.706 6.904 21058 Z= 0.552 Chirality : 0.051 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 0.00520 / 0.40 (14917) covalent geometry : angle 0.70618 / 0.55 (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 : 0.337 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: 0.5931 time to fit residues: 67.1724 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 : 0.453 ------------------------------------------------------------------------------- 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: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 2.1794 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.080833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059075 restraints weight = 40422.666| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.49 r_work: 0.2879 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14917 Z= 0.191 Angle : 0.563 8.722 21058 Z= 0.324 Chirality : 0.038 0.197 2433 Planarity : 0.005 0.040 1959 Dihedral : 22.970 174.681 4252 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.73 % Allowed : 24.02 % 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: 2.84 (0.24), residues: 1241 helix: 2.66 (0.18), residues: 800 sheet: -0.14 (0.46), residues: 134 loop : 0.83 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 156 TYR 0.015 0.002 TYR A 215 PHE 0.010 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 0.00379 / 0.19 (14917) covalent geometry : angle 0.56307 / 0.32 (21058) hydrogen bonds : bond 0.05243 / 3.55 ( 890) hydrogen bonds : angle 4.46021 / 3.34 ( 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 120 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8893 (pm20) REVERT: A 58 CYS cc_start: 0.9070 (OUTLIER) cc_final: 0.7930 (m) REVERT: A 63 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8376 (t) REVERT: A 66 MET cc_start: 0.9111 (pmt) cc_final: 0.8671 (pmt) REVERT: A 139 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8550 (mm-40) REVERT: A 143 ASP cc_start: 0.8875 (m-30) cc_final: 0.8526 (m-30) REVERT: B 66 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8887 (pmt) REVERT: B 128 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8436 (tm-30) REVERT: C 66 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.8793 (pmt) REVERT: C 139 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8333 (mm-40) REVERT: C 188 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (t0) REVERT: C 304 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8214 (mm-40) REVERT: D 139 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8568 (mm-40) REVERT: D 143 ASP cc_start: 0.8973 (m-30) cc_final: 0.8427 (m-30) outliers start: 38 outliers final: 11 residues processed: 109 average time/residue: 0.5546 time to fit residues: 66.8677 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 : 0.378 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 107 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.081295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059672 restraints weight = 40394.113| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.48 r_work: 0.2893 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0962 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= 0.165 Angle : 0.524 8.242 21058 Z= 0.302 Chirality : 0.037 0.197 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.007 176.571 4225 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.73 % Allowed : 24.80 % 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: 2.88 (0.24), residues: 1241 helix: 2.63 (0.18), residues: 805 sheet: -0.07 (0.45), residues: 136 loop : 0.96 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 194 TYR 0.021 0.002 TYR B 215 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/Z covalent geometry : bond 0.00325 / 0.17 (14917) covalent geometry : angle 0.52362 / 0.30 (21058) hydrogen bonds : bond 0.04665 / 3.17 ( 890) hydrogen bonds : angle 4.21343 / 3.16 ( 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 124 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8899 (pm20) REVERT: A 58 CYS cc_start: 0.9029 (OUTLIER) cc_final: 0.7962 (m) REVERT: A 63 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 66 MET cc_start: 0.9186 (pmt) cc_final: 0.8757 (pmt) REVERT: A 139 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8505 (mm-40) REVERT: A 143 ASP cc_start: 0.8892 (m-30) cc_final: 0.8478 (m-30) REVERT: A 261 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8874 (ptm160) REVERT: B 66 MET cc_start: 0.9160 (pmt) cc_final: 0.8714 (pmt) REVERT: C 58 CYS cc_start: 0.9004 (m) cc_final: 0.8506 (m) REVERT: C 139 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8395 (mm-40) REVERT: C 188 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8839 (t0) REVERT: C 281 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8551 (tmm160) REVERT: C 284 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 139 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8566 (mm-40) REVERT: D 143 ASP cc_start: 0.8998 (m-30) cc_final: 0.8554 (m-30) outliers start: 38 outliers final: 15 residues processed: 117 average time/residue: 0.5714 time to fit residues: 73.3614 Evaluate side-chains 98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 83 ILE 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: 30.0000 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.081300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059603 restraints weight = 40254.861| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.46 r_work: 0.2880 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14917 Z= 0.192 Angle : 0.533 7.793 21058 Z= 0.304 Chirality : 0.038 0.186 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.015 177.178 4218 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 2.81 (0.24), residues: 1241 helix: 2.56 (0.18), residues: 808 sheet: 0.01 (0.45), residues: 136 loop : 0.95 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 51 TYR 0.018 0.002 TYR D 215 PHE 0.012 0.002 PHE C 112 TRP 0.009 0.001 TRP A 121 HIS 0.006 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (14917) covalent geometry : angle 0.53321 / 0.30 (21058) hydrogen bonds : bond 0.04690 / 3.19 ( 890) hydrogen bonds : angle 4.17950 / 3.13 ( 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 112 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8926 (pm20) REVERT: A 58 CYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8098 (m) REVERT: A 66 MET cc_start: 0.9218 (pmt) cc_final: 0.8779 (pmt) REVERT: A 139 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8511 (mm-40) REVERT: A 143 ASP cc_start: 0.8915 (m-30) cc_final: 0.8506 (m-30) REVERT: A 261 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8913 (ptm160) REVERT: B 66 MET cc_start: 0.9161 (pmt) cc_final: 0.8899 (pmt) REVERT: B 139 GLN cc_start: 0.9198 (tt0) cc_final: 0.8950 (tt0) REVERT: B 143 ASP cc_start: 0.8833 (m-30) cc_final: 0.8623 (m-30) REVERT: C 58 CYS cc_start: 0.9006 (m) cc_final: 0.8512 (m) REVERT: C 139 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8374 (mm-40) REVERT: C 188 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8816 (t0) REVERT: C 284 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8630 (mm) REVERT: D 66 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9083 (pmt) outliers start: 36 outliers final: 12 residues processed: 103 average time/residue: 0.5705 time to fit residues: 64.8471 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 : 0.437 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 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: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.080267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058490 restraints weight = 40687.265| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.46 r_work: 0.2849 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14917 Z= 0.268 Angle : 0.584 7.288 21058 Z= 0.325 Chirality : 0.040 0.177 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.032 177.552 4217 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.22 % Allowed : 24.51 % 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: 2.69 (0.24), residues: 1241 helix: 2.42 (0.18), residues: 810 sheet: 0.19 (0.46), residues: 134 loop : 0.88 (0.41), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 238 TYR 0.018 0.002 TYR B 215 PHE 0.014 0.002 PHE A 112 TRP 0.010 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.27 (14917) covalent geometry : angle 0.58368 / 0.32 (21058) hydrogen bonds : bond 0.05146 / 3.51 ( 890) hydrogen bonds : angle 4.23418 / 3.18 ( 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 118 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 75 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7797 (pmm-80) REVERT: A 42 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8934 (pm20) REVERT: A 58 CYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 66 MET cc_start: 0.9234 (pmt) cc_final: 0.8794 (pmt) REVERT: A 89 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8414 (tptp) REVERT: A 108 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8830 (ttm) REVERT: A 139 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8519 (mm-40) REVERT: A 143 ASP cc_start: 0.8939 (m-30) cc_final: 0.8528 (m-30) REVERT: A 261 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8908 (ptm160) REVERT: C 58 CYS cc_start: 0.9030 (m) cc_final: 0.8533 (m) REVERT: C 139 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8421 (mm-40) REVERT: C 188 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8811 (t0) REVERT: C 281 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8510 (tmm160) REVERT: C 284 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8573 (mm) REVERT: D 139 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8676 (mm-40) REVERT: D 143 ASP cc_start: 0.9078 (m-30) cc_final: 0.8682 (m-30) REVERT: D 265 MET cc_start: 0.8757 (mmm) cc_final: 0.8497 (mmm) outliers start: 43 outliers final: 16 residues processed: 109 average time/residue: 0.5737 time to fit residues: 68.4905 Evaluate side-chains 97 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 116 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.081114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059589 restraints weight = 39932.209| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.45 r_work: 0.2889 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14917 Z= 0.159 Angle : 0.521 6.922 21058 Z= 0.298 Chirality : 0.037 0.179 2433 Planarity : 0.005 0.048 1959 Dihedral : 23.043 177.401 4213 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.63 % Allowed : 25.20 % 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: 2.78 (0.24), residues: 1241 helix: 2.51 (0.18), residues: 808 sheet: 0.23 (0.45), residues: 138 loop : 0.88 (0.41), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.015 0.002 TYR D 215 PHE 0.010 0.001 PHE C 112 TRP 0.010 0.001 TRP A 121 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (14917) covalent geometry : angle 0.52054 / 0.30 (21058) hydrogen bonds : bond 0.04401 / 3.00 ( 890) hydrogen bonds : angle 4.12955 / 3.11 ( 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 120 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7838 (pmm-80) REVERT: A 42 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: A 58 CYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8155 (m) REVERT: A 66 MET cc_start: 0.9215 (pmt) cc_final: 0.8754 (pmt) REVERT: A 89 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8407 (tptp) REVERT: A 139 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8488 (mm-40) REVERT: A 143 ASP cc_start: 0.8921 (m-30) cc_final: 0.8496 (m-30) REVERT: A 261 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8897 (ptm160) REVERT: B 66 MET cc_start: 0.9142 (pmt) cc_final: 0.8579 (pmt) REVERT: B 265 MET cc_start: 0.8562 (tpp) cc_final: 0.8034 (mmm) REVERT: C 58 CYS cc_start: 0.9044 (m) cc_final: 0.8538 (m) REVERT: C 139 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8491 (mm-40) REVERT: C 188 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8810 (t0) REVERT: C 281 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8552 (tmm160) REVERT: C 284 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8617 (mm) REVERT: D 139 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8593 (mm-40) REVERT: D 143 ASP cc_start: 0.9021 (m-30) cc_final: 0.8613 (m-30) REVERT: D 265 MET cc_start: 0.8702 (mmm) cc_final: 0.8419 (mmm) outliers start: 37 outliers final: 14 residues processed: 115 average time/residue: 0.6009 time to fit residues: 75.8664 Evaluate side-chains 98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 63 SER Chi-restraints excluded: chain C residue 68 ASP 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 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: 3.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.081534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060245 restraints weight = 40384.503| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.43 r_work: 0.2910 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14917 Z= 0.144 Angle : 0.512 7.530 21058 Z= 0.292 Chirality : 0.036 0.177 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.018 178.623 4213 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.14 % Allowed : 25.49 % 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: 2.85 (0.25), residues: 1241 helix: 2.57 (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 0.005 0.000 ARG D 51 TYR 0.019 0.002 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 0.00283 / 0.14 (14917) covalent geometry : angle 0.51158 / 0.29 (21058) hydrogen bonds : bond 0.04247 / 2.90 ( 890) hydrogen bonds : angle 4.06504 / 3.07 ( 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: 32 poor density : 83 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8898 (pm20) REVERT: A 58 CYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8166 (m) REVERT: A 66 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8757 (pmt) REVERT: A 89 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8431 (tptp) REVERT: A 139 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8510 (mm-40) REVERT: A 143 ASP cc_start: 0.8907 (m-30) cc_final: 0.8485 (m-30) REVERT: A 261 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8897 (ptm160) REVERT: B 265 MET cc_start: 0.8611 (tpp) cc_final: 0.8010 (mmm) REVERT: C 58 CYS cc_start: 0.9036 (m) cc_final: 0.8571 (m) REVERT: C 139 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8418 (mm-40) REVERT: C 188 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8822 (t0) REVERT: C 281 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8586 (tmm160) REVERT: C 284 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8678 (mm) REVERT: D 139 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8586 (mm-40) REVERT: D 143 ASP cc_start: 0.8982 (m-30) cc_final: 0.8577 (m-30) outliers start: 32 outliers final: 13 residues processed: 109 average time/residue: 0.6155 time to fit residues: 73.5718 Evaluate side-chains 97 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 13 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 68 ASP 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 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 259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.080936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059571 restraints weight = 40546.457| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.43 r_work: 0.2893 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14917 Z= 0.189 Angle : 0.538 7.258 21058 Z= 0.303 Chirality : 0.037 0.176 2433 Planarity : 0.004 0.041 1959 Dihedral : 23.015 179.277 4212 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.65 % Allowed : 26.27 % Favored : 71.08 % 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: 2.80 (0.25), residues: 1241 helix: 2.53 (0.18), residues: 808 sheet: 0.27 (0.45), residues: 138 loop : 0.87 (0.41), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 51 TYR 0.022 0.002 TYR D 215 PHE 0.011 0.002 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 0.00385 / 0.19 (14917) covalent geometry : angle 0.53830 / 0.30 (21058) hydrogen bonds : bond 0.04468 / 3.05 ( 890) hydrogen bonds : angle 4.08075 / 3.08 ( 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 99 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7855 (pmm-80) REVERT: A 42 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8908 (pm20) REVERT: A 58 CYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8212 (m) REVERT: A 66 MET cc_start: 0.9223 (pmt) cc_final: 0.8764 (pmt) REVERT: A 89 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8446 (tptp) REVERT: A 139 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8532 (mm-40) REVERT: A 143 ASP cc_start: 0.8928 (m-30) cc_final: 0.8509 (m-30) REVERT: A 261 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8914 (ptm160) REVERT: C 58 CYS cc_start: 0.9035 (m) cc_final: 0.8580 (m) REVERT: C 139 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8427 (mm-40) REVERT: C 281 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8597 (tmm160) REVERT: C 284 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8671 (mm) REVERT: D 265 MET cc_start: 0.8794 (mmm) cc_final: 0.8417 (mmm) outliers start: 27 outliers final: 14 residues processed: 97 average time/residue: 0.5669 time to fit residues: 60.3279 Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 269 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 72 HIS 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 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: 3.9990 chunk 119 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** 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 = 0.3534 r_free = 0.3534 target = 0.079896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058328 restraints weight = 40947.062| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.45 r_work: 0.2857 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1408 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= 0.273 Angle : 0.601 7.142 21058 Z= 0.331 Chirality : 0.041 0.189 2433 Planarity : 0.005 0.042 1959 Dihedral : 23.019 179.521 4210 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.94 % Allowed : 26.18 % Favored : 70.88 % 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: 2.41 (0.18), residues: 809 sheet: 0.21 (0.44), residues: 138 loop : 0.81 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 51 TYR 0.018 0.002 TYR A 307 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 0.00565 / 0.27 (14917) covalent geometry : angle 0.60150 / 0.33 (21058) hydrogen bonds : bond 0.05053 / 3.45 ( 890) hydrogen bonds : angle 4.19885 / 3.17 ( 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 103 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7882 (pmm-80) REVERT: A 42 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8930 (pm20) REVERT: A 58 CYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8217 (m) REVERT: A 66 MET cc_start: 0.9239 (pmt) cc_final: 0.8794 (pmt) REVERT: A 89 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8486 (tptp) REVERT: A 139 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8551 (mm-40) REVERT: A 143 ASP cc_start: 0.8925 (m-30) cc_final: 0.8528 (m-30) REVERT: A 261 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8901 (ptm160) REVERT: B 139 GLN cc_start: 0.9242 (tt0) cc_final: 0.8753 (tm-30) REVERT: B 143 ASP cc_start: 0.9034 (m-30) cc_final: 0.8365 (m-30) REVERT: B 265 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: B 298 MET cc_start: 0.9580 (tpt) cc_final: 0.8711 (tpt) REVERT: C 58 CYS cc_start: 0.9060 (m) cc_final: 0.8594 (m) REVERT: C 139 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8588 (mm-40) REVERT: C 281 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8584 (tmm160) REVERT: C 284 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8669 (mm) REVERT: D 139 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8841 (mm-40) REVERT: D 143 ASP cc_start: 0.9024 (m-30) cc_final: 0.8707 (m-30) REVERT: D 265 MET cc_start: 0.8903 (mmm) cc_final: 0.8258 (mmm) outliers start: 30 outliers final: 14 residues processed: 98 average time/residue: 0.5722 time to fit residues: 61.2381 Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 269 VAL 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 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: 0.8980 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: 0.4980 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.081329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059947 restraints weight = 40448.196| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.44 r_work: 0.2902 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14917 Z= 0.158 Angle : 0.533 8.632 21058 Z= 0.302 Chirality : 0.037 0.183 2433 Planarity : 0.005 0.041 1959 Dihedral : 23.017 179.033 4210 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.35 % Allowed : 26.86 % Favored : 70.78 % 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: 2.74 (0.25), residues: 1241 helix: 2.50 (0.18), residues: 808 sheet: 0.19 (0.45), residues: 138 loop : 0.82 (0.41), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 51 TYR 0.014 0.001 TYR A 307 PHE 0.009 0.001 PHE A 112 TRP 0.011 0.001 TRP A 121 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (14917) covalent geometry : angle 0.53318 / 0.30 (21058) hydrogen bonds : bond 0.04252 / 2.91 ( 890) hydrogen bonds : angle 4.09667 / 3.10 ( 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 103 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7871 (pmm-80) REVERT: A 42 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8912 (pm20) REVERT: A 58 CYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8111 (m) REVERT: A 66 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8762 (pmt) REVERT: A 89 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8423 (tptp) REVERT: A 139 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8501 (mm-40) REVERT: A 143 ASP cc_start: 0.8919 (m-30) cc_final: 0.8491 (m-30) REVERT: A 261 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8885 (ptm160) REVERT: B 139 GLN cc_start: 0.9226 (tt0) cc_final: 0.8719 (tm-30) REVERT: B 143 ASP cc_start: 0.8991 (m-30) cc_final: 0.8247 (m-30) REVERT: B 265 MET cc_start: 0.8478 (tpp) cc_final: 0.8095 (mmm) REVERT: C 58 CYS cc_start: 0.9028 (m) cc_final: 0.8536 (m) REVERT: C 139 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8618 (mm-40) REVERT: C 284 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8677 (mm) REVERT: D 139 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8797 (mm-40) REVERT: D 143 ASP cc_start: 0.8950 (m-30) cc_final: 0.8596 (m-30) REVERT: D 265 MET cc_start: 0.8781 (mmm) cc_final: 0.8197 (mmm) outliers start: 24 outliers final: 10 residues processed: 99 average time/residue: 0.5597 time to fit residues: 61.0578 Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 13 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 251 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 130 optimal weight: 50.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 84 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.080389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058970 restraints weight = 40422.941| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.43 r_work: 0.2875 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14917 Z= 0.223 Angle : 0.564 8.605 21058 Z= 0.314 Chirality : 0.039 0.192 2433 Planarity : 0.005 0.041 1959 Dihedral : 22.996 179.544 4208 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.25 % Allowed : 26.86 % Favored : 70.88 % 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: 2.70 (0.25), residues: 1241 helix: 2.48 (0.18), residues: 809 sheet: 0.06 (0.44), residues: 140 loop : 0.84 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 51 TYR 0.020 0.002 TYR A 307 PHE 0.012 0.002 PHE C 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 0.00461 / 0.22 (14917) covalent geometry : angle 0.56375 / 0.31 (21058) hydrogen bonds : bond 0.04686 / 3.20 ( 890) hydrogen bonds : angle 4.13064 / 3.13 ( 2415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.48 seconds wall clock time: 59 minutes 36.71 seconds (3576.71 seconds total)