Starting phenix.real_space_refine on Fri Jul 3 15:39:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuo_35728/07_2026/8iuo_35728.map" } resolution = 3.96 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= 0.007 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 85 5.16 5 C 9225 2.51 5 N 2530 2.21 5 O 2910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s 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: 14785 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "A" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "F" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'RNA': 35} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 30} Link IDs: {'rna2p': 5, 'rna3p': 29} Chain: "B" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "D" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "E" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Time building chain proxies: 3.59, per 1000 atoms: 0.24 Number of scatterers: 14785 At special positions: 0 Unit cell: (171.7, 147.05, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 35 15.00 O 2910 8.00 N 2530 7.00 C 9225 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: 1.28 Conformation dependent library (CDL) restraints added in 640.4 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 71.5% alpha, 5.0% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS C 5 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 120 through 140 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 171 removed outlier: 3.711A pdb=" N ILE C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.961A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 268 removed outlier: 3.947A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 311 " --> pdb=" O LYS C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 4.003A pdb=" N GLN C 316 " --> pdb=" O SER C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 3.776A pdb=" N ASN C 360 " --> pdb=" O GLN C 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS A 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 120 through 140 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.720A pdb=" N ARG A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.711A pdb=" N ILE A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.962A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.611A pdb=" N ALA A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.946A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.003A pdb=" N GLN A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.776A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS B 5 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 120 through 140 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.712A pdb=" N ILE B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.962A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.947A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 4.004A pdb=" N GLN B 316 " --> pdb=" O SER B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.776A pdb=" N ASN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS D 5 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 120 through 140 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG D 150 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 171 removed outlier: 3.711A pdb=" N ILE D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 217 through 233 removed outlier: 3.962A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.947A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 removed outlier: 4.003A pdb=" N GLN D 316 " --> pdb=" O SER D 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.777A pdb=" N ASN D 360 " --> pdb=" O GLN D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS E 5 " --> pdb=" O ALA E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 87 Processing helix chain 'E' and resid 120 through 140 Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG E 150 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.712A pdb=" N ILE E 163 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 217 through 233 removed outlier: 3.961A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.946A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 311 " --> pdb=" O LYS E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 removed outlier: 4.004A pdb=" N GLN E 316 " --> pdb=" O SER E 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 316' Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.777A pdb=" N ASN E 360 " --> pdb=" O GLN E 356 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 104 removed outlier: 4.196A pdb=" N ASP C 96 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 104 removed outlier: 4.195A pdb=" N ASP A 96 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 104 removed outlier: 4.195A pdb=" N ASP B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 104 removed outlier: 4.197A pdb=" N ASP D 96 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 104 removed outlier: 4.196A pdb=" N ASP E 96 " --> pdb=" O THR E 115 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4620 1.34 - 1.45: 2287 1.45 - 1.57: 7958 1.57 - 1.69: 69 1.69 - 1.81: 155 Bond restraints: 15089 Sorted by residual: bond pdb=" N GLY E 236 " pdb=" CA GLY E 236 " ideal model delta sigma weight residual 1.443 1.478 -0.035 1.17e-02 7.31e+03 8.81e+00 bond pdb=" N VAL E 239 " pdb=" CA VAL E 239 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N VAL C 239 " pdb=" CA VAL C 239 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.31e+00 bond pdb=" N SER D 237 " pdb=" CA SER D 237 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.17e-02 7.31e+03 8.23e+00 bond pdb=" N VAL B 239 " pdb=" CA VAL B 239 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.22e+00 ... (remaining 15084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 19055 1.31 - 2.63: 1174 2.63 - 3.94: 159 3.94 - 5.25: 56 5.25 - 6.56: 17 Bond angle restraints: 20461 Sorted by residual: angle pdb=" CA GLY A 236 " pdb=" C GLY A 236 " pdb=" O GLY A 236 " ideal model delta sigma weight residual 122.16 118.07 4.09 8.20e-01 1.49e+00 2.48e+01 angle pdb=" N ASN C 187 " pdb=" CA ASN C 187 " pdb=" C ASN C 187 " ideal model delta sigma weight residual 113.50 108.24 5.26 1.23e+00 6.61e-01 1.83e+01 angle pdb=" N ARG A 234 " pdb=" CA ARG A 234 " pdb=" C ARG A 234 " ideal model delta sigma weight residual 113.61 107.83 5.78 1.50e+00 4.44e-01 1.48e+01 angle pdb=" O3' U F1014 " pdb=" C3' U F1014 " pdb=" C2' U F1014 " ideal model delta sigma weight residual 113.70 118.87 -5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" C ILE D 104 " pdb=" N ASN D 105 " pdb=" CA ASN D 105 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 ... (remaining 20456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 8847 34.98 - 69.96: 216 69.96 - 104.94: 15 104.94 - 139.92: 3 139.92 - 174.89: 1 Dihedral angle restraints: 9082 sinusoidal: 3892 harmonic: 5190 Sorted by residual: dihedral pdb=" C4' U F1028 " pdb=" C3' U F1028 " pdb=" O3' U F1028 " pdb=" P U F1029 " ideal model delta sinusoidal sigma weight residual 220.00 45.11 174.89 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA SER E 153 " pdb=" C SER E 153 " pdb=" N PRO E 154 " pdb=" CA PRO E 154 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER C 153 " pdb=" C SER C 153 " pdb=" N PRO C 154 " pdb=" CA PRO C 154 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 9079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1790 0.047 - 0.094: 457 0.094 - 0.141: 75 0.141 - 0.189: 9 0.189 - 0.236: 4 Chirality restraints: 2335 Sorted by residual: chirality pdb=" C3' U F1021 " pdb=" C4' U F1021 " pdb=" O3' U F1021 " pdb=" C2' U F1021 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C3' U F1007 " pdb=" C4' U F1007 " pdb=" O3' U F1007 " pdb=" C2' U F1007 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' U F1014 " pdb=" C4' U F1014 " pdb=" O3' U F1014 " pdb=" C2' U F1014 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2332 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 215 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LYS C 215 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C 215 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS C 216 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 215 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C LYS B 215 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS B 215 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS B 216 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 215 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C LYS A 215 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS A 215 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS A 216 " -0.014 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 387 2.69 - 3.24: 16470 3.24 - 3.80: 24264 3.80 - 4.35: 28856 4.35 - 4.90: 47479 Nonbonded interactions: 117456 Sorted by model distance: nonbonded pdb=" O2' U F1028 " pdb=" OP1 U F1029 " model vdw 2.141 3.040 nonbonded pdb=" OP2 U F1008 " pdb=" ND2 ASN E 188 " model vdw 2.203 3.120 nonbonded pdb=" OP2 U F1029 " pdb=" ND2 ASN D 188 " model vdw 2.216 3.120 nonbonded pdb=" OP2 U F1022 " pdb=" ND2 ASN B 188 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG A 184 " pdb=" OP1 U F1035 " model vdw 2.239 3.120 ... (remaining 117451 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 6.190 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.830 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.008 0.052 15089 Z= 0.370 Angle : 0.738 6.563 20461 Z= 0.443 Chirality : 0.043 0.236 2335 Planarity : 0.004 0.046 2510 Dihedral : 15.591 174.894 5772 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.19 % Allowed : 2.79 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.18), residues: 1800 helix: -0.79 (0.13), residues: 1165 sheet: -3.72 (0.41), residues: 125 loop : -2.70 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 27 TYR 0.010 0.001 TYR C 210 PHE 0.011 0.001 PHE A 247 TRP 0.002 0.001 TRP D 260 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.37 (15089) covalent geometry : angle 0.73764 / 0.44 (20461) hydrogen bonds : bond 0.13710 / 9.19 ( 880) hydrogen bonds : angle 4.77197 / 3.52 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 MET cc_start: 0.7972 (ptp) cc_final: 0.7408 (ptm) REVERT: C 271 MET cc_start: 0.9268 (mmm) cc_final: 0.8521 (mtp) REVERT: C 315 THR cc_start: 0.8675 (m) cc_final: 0.8434 (m) REVERT: A 194 MET cc_start: 0.7853 (mtm) cc_final: 0.7582 (mtt) REVERT: B 158 MET cc_start: 0.8021 (mmm) cc_final: 0.7776 (mmm) REVERT: B 286 GLU cc_start: 0.7953 (tp30) cc_final: 0.7261 (tp30) REVERT: B 297 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 305 ASN cc_start: 0.7947 (m-40) cc_final: 0.7445 (p0) REVERT: D 50 MET cc_start: 0.8635 (mtt) cc_final: 0.8327 (mtm) REVERT: D 71 MET cc_start: 0.8935 (mtm) cc_final: 0.8705 (mtt) REVERT: D 142 MET cc_start: 0.8464 (ptp) cc_final: 0.7780 (ptp) REVERT: D 263 LEU cc_start: 0.8843 (tp) cc_final: 0.8578 (tt) REVERT: E 134 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7402 (m) REVERT: E 216 HIS cc_start: 0.5384 (OUTLIER) cc_final: 0.5088 (m-70) outliers start: 33 outliers final: 9 residues processed: 234 average time/residue: 0.1523 time to fit residues: 49.6710 Evaluate side-chains 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 216 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS D 16 GLN E 230 GLN E 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049623 restraints weight = 78648.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051042 restraints weight = 43011.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051984 restraints weight = 28859.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052630 restraints weight = 22144.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052976 restraints weight = 18561.267| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15089 Z= 0.152 Angle : 0.595 9.126 20461 Z= 0.314 Chirality : 0.041 0.245 2335 Planarity : 0.004 0.035 2510 Dihedral : 8.328 159.351 2393 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.46 % Allowed : 9.37 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1800 helix: 0.80 (0.15), residues: 1205 sheet: -3.18 (0.38), residues: 125 loop : -2.60 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.012 0.001 TYR C 88 PHE 0.011 0.001 PHE D 111 TRP 0.005 0.001 TRP E 260 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (15089) covalent geometry : angle 0.59502 / 0.31 (20461) hydrogen bonds : bond 0.03612 / 2.42 ( 880) hydrogen bonds : angle 3.77971 / 2.67 ( 2520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8923 (mtp) cc_final: 0.8598 (mtp) REVERT: C 105 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.5997 (p0) REVERT: C 271 MET cc_start: 0.9300 (mmm) cc_final: 0.8530 (mtp) REVERT: A 109 MET cc_start: 0.6608 (mmt) cc_final: 0.6216 (mmp) REVERT: A 194 MET cc_start: 0.8048 (mtm) cc_final: 0.7734 (mtm) REVERT: B 50 MET cc_start: 0.8975 (mtp) cc_final: 0.8410 (ttm) REVERT: B 101 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8970 (mmt-90) REVERT: B 271 MET cc_start: 0.8463 (mtp) cc_final: 0.8144 (mtp) REVERT: B 297 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7237 (tm-30) REVERT: B 305 ASN cc_start: 0.7960 (m-40) cc_final: 0.7473 (p0) REVERT: D 50 MET cc_start: 0.8740 (mtt) cc_final: 0.8414 (mtm) REVERT: D 67 MET cc_start: 0.9361 (mmm) cc_final: 0.8629 (mmm) REVERT: D 71 MET cc_start: 0.9064 (mtm) cc_final: 0.8528 (mtm) REVERT: D 158 MET cc_start: 0.8747 (mmt) cc_final: 0.7844 (mmt) REVERT: D 162 CYS cc_start: 0.9117 (m) cc_final: 0.8910 (m) REVERT: D 263 LEU cc_start: 0.8938 (tp) cc_final: 0.8704 (tt) REVERT: E 9 ASN cc_start: 0.8602 (t0) cc_final: 0.8276 (t0) REVERT: E 286 GLU cc_start: 0.8602 (tt0) cc_final: 0.8175 (tm-30) REVERT: E 289 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8920 (mm-30) REVERT: E 297 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7016 (tm-30) outliers start: 22 outliers final: 8 residues processed: 153 average time/residue: 0.1287 time to fit residues: 28.5131 Evaluate side-chains 121 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 116 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 33 optimal weight: 0.0040 chunk 150 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN C 124 GLN C 230 GLN A 9 ASN D 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048597 restraints weight = 79039.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.050011 restraints weight = 43011.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050959 restraints weight = 28731.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051588 restraints weight = 21949.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051935 restraints weight = 18404.294| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15089 Z= 0.125 Angle : 0.543 8.266 20461 Z= 0.285 Chirality : 0.039 0.247 2335 Planarity : 0.003 0.032 2510 Dihedral : 8.113 160.864 2378 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.53 % Allowed : 11.76 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1800 helix: 1.38 (0.15), residues: 1175 sheet: -1.62 (0.53), residues: 70 loop : -2.45 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 84 TYR 0.010 0.001 TYR B 288 PHE 0.027 0.001 PHE B 223 TRP 0.004 0.001 TRP E 260 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (15089) covalent geometry : angle 0.54271 / 0.29 (20461) hydrogen bonds : bond 0.03408 / 2.30 ( 880) hydrogen bonds : angle 3.51910 / 2.45 ( 2520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASN cc_start: 0.8633 (t0) cc_final: 0.8219 (t0) REVERT: C 50 MET cc_start: 0.8919 (mtp) cc_final: 0.8585 (mtp) REVERT: C 271 MET cc_start: 0.9351 (mmm) cc_final: 0.9145 (mmp) REVERT: A 109 MET cc_start: 0.6707 (mmt) cc_final: 0.6404 (mmp) REVERT: A 194 MET cc_start: 0.8011 (mtm) cc_final: 0.7763 (mtt) REVERT: A 281 MET cc_start: 0.8049 (mmm) cc_final: 0.7706 (tpt) REVERT: B 50 MET cc_start: 0.8933 (mtp) cc_final: 0.8731 (ttm) REVERT: B 71 MET cc_start: 0.9209 (mtm) cc_final: 0.8892 (mtm) REVERT: B 297 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 305 ASN cc_start: 0.8193 (m-40) cc_final: 0.7638 (p0) REVERT: D 50 MET cc_start: 0.8745 (mtt) cc_final: 0.8451 (mtm) REVERT: D 67 MET cc_start: 0.9387 (mmm) cc_final: 0.8606 (mmm) REVERT: D 71 MET cc_start: 0.9059 (mtm) cc_final: 0.8535 (mtm) REVERT: D 138 MET cc_start: 0.9091 (tpp) cc_final: 0.8697 (tmm) REVERT: D 142 MET cc_start: 0.8321 (ptp) cc_final: 0.8042 (pmm) REVERT: D 162 CYS cc_start: 0.9120 (m) cc_final: 0.8908 (m) REVERT: E 9 ASN cc_start: 0.8660 (t0) cc_final: 0.8350 (t0) REVERT: E 289 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8893 (mm-30) REVERT: E 297 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7007 (tm-30) outliers start: 23 outliers final: 12 residues processed: 139 average time/residue: 0.1251 time to fit residues: 25.9409 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS D 58 ASN E 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047361 restraints weight = 79012.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048750 restraints weight = 42848.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049652 restraints weight = 28660.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050295 restraints weight = 22005.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050600 restraints weight = 18358.908| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15089 Z= 0.132 Angle : 0.551 7.920 20461 Z= 0.286 Chirality : 0.039 0.250 2335 Planarity : 0.003 0.042 2510 Dihedral : 8.063 159.340 2377 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.53 % Allowed : 12.96 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1800 helix: 1.57 (0.15), residues: 1175 sheet: -1.14 (0.58), residues: 70 loop : -2.27 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.010 0.001 TYR E 347 PHE 0.016 0.001 PHE B 223 TRP 0.003 0.001 TRP E 260 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15089) covalent geometry : angle 0.55072 / 0.29 (20461) hydrogen bonds : bond 0.03381 / 2.29 ( 880) hydrogen bonds : angle 3.52804 / 2.45 ( 2520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8932 (mtp) cc_final: 0.8589 (mtp) REVERT: C 105 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.5782 (p0) REVERT: C 271 MET cc_start: 0.9387 (mmm) cc_final: 0.9175 (mmp) REVERT: A 48 CYS cc_start: 0.8036 (m) cc_final: 0.7605 (t) REVERT: A 109 MET cc_start: 0.6692 (mmt) cc_final: 0.6375 (mmp) REVERT: A 194 MET cc_start: 0.8058 (mtm) cc_final: 0.7786 (mtt) REVERT: A 281 MET cc_start: 0.8000 (mmm) cc_final: 0.7789 (tpt) REVERT: B 162 CYS cc_start: 0.9297 (m) cc_final: 0.8944 (m) REVERT: B 297 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 305 ASN cc_start: 0.8419 (m-40) cc_final: 0.7720 (p0) REVERT: D 50 MET cc_start: 0.8777 (mtt) cc_final: 0.8499 (mtm) REVERT: D 67 MET cc_start: 0.9397 (mmm) cc_final: 0.8647 (mmm) REVERT: D 71 MET cc_start: 0.9096 (mtm) cc_final: 0.8530 (mtm) REVERT: D 158 MET cc_start: 0.8684 (mmt) cc_final: 0.7950 (mmp) REVERT: D 162 CYS cc_start: 0.9138 (m) cc_final: 0.8908 (m) REVERT: E 138 MET cc_start: 0.9239 (mmm) cc_final: 0.9028 (mmm) REVERT: E 221 ASP cc_start: 0.9087 (m-30) cc_final: 0.8875 (t70) REVERT: E 282 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8039 (tm-30) REVERT: E 289 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8901 (mm-30) REVERT: E 297 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7158 (tm-30) outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 0.1134 time to fit residues: 23.2121 Evaluate side-chains 118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 129 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 143 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** 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 = 0.3346 r_free = 0.3346 target = 0.062742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048091 restraints weight = 78507.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049482 restraints weight = 42412.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050432 restraints weight = 28344.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050954 restraints weight = 21659.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051456 restraints weight = 18316.912| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15089 Z= 0.100 Angle : 0.510 9.321 20461 Z= 0.264 Chirality : 0.038 0.240 2335 Planarity : 0.003 0.034 2510 Dihedral : 7.970 159.629 2377 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.00 % Allowed : 14.15 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1800 helix: 1.69 (0.15), residues: 1175 sheet: -0.89 (0.57), residues: 70 loop : -2.11 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 101 TYR 0.012 0.001 TYR C 23 PHE 0.014 0.001 PHE B 223 TRP 0.002 0.001 TRP D 260 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (15089) covalent geometry : angle 0.51001 / 0.26 (20461) hydrogen bonds : bond 0.02985 / 2.01 ( 880) hydrogen bonds : angle 3.34502 / 2.31 ( 2520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8917 (mtp) cc_final: 0.8557 (mtp) REVERT: C 271 MET cc_start: 0.9382 (mmm) cc_final: 0.9008 (mmp) REVERT: A 48 CYS cc_start: 0.8098 (m) cc_final: 0.7650 (t) REVERT: A 109 MET cc_start: 0.6745 (mmt) cc_final: 0.6457 (mmp) REVERT: A 281 MET cc_start: 0.7984 (mmm) cc_final: 0.7731 (tpt) REVERT: B 71 MET cc_start: 0.9213 (mtm) cc_final: 0.8938 (mtm) REVERT: B 162 CYS cc_start: 0.9321 (m) cc_final: 0.8983 (m) REVERT: B 297 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 305 ASN cc_start: 0.8415 (m-40) cc_final: 0.7721 (p0) REVERT: D 50 MET cc_start: 0.8737 (mtt) cc_final: 0.8462 (mtm) REVERT: D 67 MET cc_start: 0.9367 (mmm) cc_final: 0.8594 (mmm) REVERT: D 71 MET cc_start: 0.9086 (mtm) cc_final: 0.8578 (mtm) REVERT: D 138 MET cc_start: 0.9137 (tpp) cc_final: 0.8902 (tmm) REVERT: D 162 CYS cc_start: 0.9151 (m) cc_final: 0.8914 (m) REVERT: E 289 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8891 (mm-30) REVERT: E 297 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7189 (tm-30) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.1128 time to fit residues: 21.7295 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 69 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 177 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** 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 = 0.3314 r_free = 0.3314 target = 0.061371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.046647 restraints weight = 78672.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047975 restraints weight = 43492.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048849 restraints weight = 29609.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.049455 restraints weight = 22975.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.049855 restraints weight = 19453.697| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15089 Z= 0.125 Angle : 0.542 10.140 20461 Z= 0.279 Chirality : 0.039 0.248 2335 Planarity : 0.003 0.030 2510 Dihedral : 7.986 159.181 2377 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.06 % Allowed : 14.95 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1800 helix: 1.84 (0.15), residues: 1160 sheet: -0.62 (0.57), residues: 70 loop : -2.12 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.009 0.001 TYR E 347 PHE 0.011 0.001 PHE B 223 TRP 0.002 0.001 TRP E 260 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15089) covalent geometry : angle 0.54162 / 0.28 (20461) hydrogen bonds : bond 0.03294 / 2.23 ( 880) hydrogen bonds : angle 3.43362 / 2.39 ( 2520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8991 (mtp) cc_final: 0.8621 (mtp) REVERT: C 105 ASN cc_start: 0.6620 (OUTLIER) cc_final: 0.5711 (p0) REVERT: C 271 MET cc_start: 0.9384 (mmm) cc_final: 0.9036 (mmp) REVERT: A 48 CYS cc_start: 0.8040 (m) cc_final: 0.7691 (t) REVERT: A 109 MET cc_start: 0.6703 (mmt) cc_final: 0.6406 (mmp) REVERT: A 257 MET cc_start: 0.8734 (mmt) cc_final: 0.8381 (mmt) REVERT: B 71 MET cc_start: 0.9252 (mtm) cc_final: 0.8839 (mtm) REVERT: B 162 CYS cc_start: 0.9340 (m) cc_final: 0.8979 (m) REVERT: B 271 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7569 (mtp) REVERT: B 297 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 305 ASN cc_start: 0.8547 (m-40) cc_final: 0.7681 (p0) REVERT: D 50 MET cc_start: 0.8762 (mtt) cc_final: 0.8506 (mtp) REVERT: D 67 MET cc_start: 0.9392 (mmm) cc_final: 0.8673 (mmm) REVERT: D 71 MET cc_start: 0.9099 (mtm) cc_final: 0.8524 (mtm) REVERT: D 138 MET cc_start: 0.9149 (tpp) cc_final: 0.8943 (tmm) REVERT: D 162 CYS cc_start: 0.9144 (m) cc_final: 0.8721 (t) REVERT: E 289 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8910 (mm-30) REVERT: E 297 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7251 (tm-30) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.1186 time to fit residues: 21.6335 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 4 optimal weight: 0.3980 chunk 162 optimal weight: 0.0370 chunk 174 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN C 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048870 restraints weight = 78500.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050161 restraints weight = 43985.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051041 restraints weight = 30055.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051616 restraints weight = 23355.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051933 restraints weight = 19775.181| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15089 Z= 0.095 Angle : 0.531 10.669 20461 Z= 0.267 Chirality : 0.037 0.236 2335 Planarity : 0.003 0.028 2510 Dihedral : 7.903 159.215 2377 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.20 % Allowed : 15.48 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1800 helix: 1.88 (0.15), residues: 1165 sheet: -0.38 (0.57), residues: 70 loop : -2.00 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.007 0.001 TYR E 135 PHE 0.010 0.001 PHE B 223 TRP 0.002 0.001 TRP B 260 HIS 0.002 0.000 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (15089) covalent geometry : angle 0.53142 / 0.27 (20461) hydrogen bonds : bond 0.02833 / 1.92 ( 880) hydrogen bonds : angle 3.25315 / 2.25 ( 2520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8900 (mtp) cc_final: 0.8530 (mtp) REVERT: C 105 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.5653 (p0) REVERT: C 271 MET cc_start: 0.9383 (mmm) cc_final: 0.9023 (mmp) REVERT: A 48 CYS cc_start: 0.8005 (m) cc_final: 0.7762 (t) REVERT: A 50 MET cc_start: 0.7645 (ptp) cc_final: 0.7359 (ppp) REVERT: A 74 LEU cc_start: 0.8771 (tp) cc_final: 0.8446 (tt) REVERT: A 109 MET cc_start: 0.6690 (mmt) cc_final: 0.6389 (mmp) REVERT: A 257 MET cc_start: 0.8661 (mmt) cc_final: 0.8358 (mmt) REVERT: A 281 MET cc_start: 0.8166 (tpp) cc_final: 0.7919 (tpt) REVERT: B 71 MET cc_start: 0.9109 (mtm) cc_final: 0.8872 (mtm) REVERT: B 162 CYS cc_start: 0.9253 (m) cc_final: 0.8910 (m) REVERT: B 271 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7445 (mtp) REVERT: B 297 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 305 ASN cc_start: 0.8446 (m-40) cc_final: 0.7697 (p0) REVERT: D 50 MET cc_start: 0.8666 (mtt) cc_final: 0.8395 (mtp) REVERT: D 67 MET cc_start: 0.9303 (mmm) cc_final: 0.8559 (mmm) REVERT: D 71 MET cc_start: 0.9035 (mtm) cc_final: 0.8553 (mtm) REVERT: D 142 MET cc_start: 0.8104 (ptt) cc_final: 0.7059 (ppp) REVERT: E 67 MET cc_start: 0.8589 (mmm) cc_final: 0.8355 (mmt) REVERT: E 109 MET cc_start: 0.7528 (tpp) cc_final: 0.6723 (mtt) REVERT: E 289 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8835 (mm-30) REVERT: E 297 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7191 (tm-30) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.1018 time to fit residues: 20.3124 Evaluate side-chains 118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.0000 chunk 82 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048905 restraints weight = 78442.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050299 restraints weight = 42201.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051214 restraints weight = 28158.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051861 restraints weight = 21655.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052241 restraints weight = 18166.403| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15089 Z= 0.096 Angle : 0.550 12.493 20461 Z= 0.272 Chirality : 0.037 0.234 2335 Planarity : 0.003 0.027 2510 Dihedral : 7.898 158.940 2377 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.26 % Allowed : 16.21 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1800 helix: 1.95 (0.15), residues: 1160 sheet: -0.25 (0.57), residues: 70 loop : -1.98 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.006 0.001 TYR B 288 PHE 0.009 0.001 PHE B 223 TRP 0.002 0.000 TRP B 260 HIS 0.003 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (15089) covalent geometry : angle 0.55022 / 0.27 (20461) hydrogen bonds : bond 0.02776 / 1.88 ( 880) hydrogen bonds : angle 3.24131 / 2.24 ( 2520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8948 (mtp) cc_final: 0.8550 (mtp) REVERT: C 105 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.5757 (p0) REVERT: C 109 MET cc_start: 0.7385 (mmm) cc_final: 0.7184 (tpt) REVERT: C 271 MET cc_start: 0.9403 (mmm) cc_final: 0.9190 (mmp) REVERT: A 48 CYS cc_start: 0.8007 (m) cc_final: 0.7783 (t) REVERT: A 50 MET cc_start: 0.7646 (ptp) cc_final: 0.7377 (ppp) REVERT: A 74 LEU cc_start: 0.8777 (tp) cc_final: 0.8439 (tt) REVERT: A 109 MET cc_start: 0.6633 (mmt) cc_final: 0.6353 (mmp) REVERT: A 194 MET cc_start: 0.7893 (mtm) cc_final: 0.7347 (mtm) REVERT: A 257 MET cc_start: 0.8724 (mmt) cc_final: 0.8476 (mmt) REVERT: A 281 MET cc_start: 0.8240 (tpp) cc_final: 0.7977 (tpt) REVERT: B 162 CYS cc_start: 0.9310 (m) cc_final: 0.8967 (m) REVERT: B 297 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 305 ASN cc_start: 0.8518 (m-40) cc_final: 0.7726 (p0) REVERT: D 50 MET cc_start: 0.8681 (mtt) cc_final: 0.8408 (mtp) REVERT: D 67 MET cc_start: 0.9327 (mmm) cc_final: 0.8561 (mmm) REVERT: D 71 MET cc_start: 0.9097 (mtm) cc_final: 0.8632 (mtm) REVERT: D 138 MET cc_start: 0.9200 (tmm) cc_final: 0.8957 (tmm) REVERT: D 142 MET cc_start: 0.8144 (ptt) cc_final: 0.6779 (ppp) REVERT: E 67 MET cc_start: 0.8662 (mmm) cc_final: 0.8428 (mmt) REVERT: E 109 MET cc_start: 0.7599 (tpp) cc_final: 0.6744 (mtt) REVERT: E 289 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8892 (mm-30) REVERT: E 297 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7124 (tm-30) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.1193 time to fit residues: 22.6898 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 67 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047145 restraints weight = 79489.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048409 restraints weight = 44641.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049271 restraints weight = 30752.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049837 restraints weight = 23942.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050206 restraints weight = 20373.015| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15089 Z= 0.136 Angle : 0.575 10.069 20461 Z= 0.290 Chirality : 0.039 0.249 2335 Planarity : 0.003 0.029 2510 Dihedral : 7.979 158.718 2377 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.20 % Allowed : 16.28 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1800 helix: 1.73 (0.15), residues: 1195 sheet: -0.22 (0.59), residues: 70 loop : -2.29 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 101 TYR 0.011 0.001 TYR E 347 PHE 0.010 0.001 PHE C 219 TRP 0.003 0.001 TRP D 260 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15089) covalent geometry : angle 0.57549 / 0.29 (20461) hydrogen bonds : bond 0.03355 / 2.26 ( 880) hydrogen bonds : angle 3.45040 / 2.40 ( 2520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8905 (mtp) cc_final: 0.8552 (mtp) REVERT: C 105 ASN cc_start: 0.6628 (OUTLIER) cc_final: 0.5727 (p0) REVERT: C 271 MET cc_start: 0.9392 (mmm) cc_final: 0.8900 (tpp) REVERT: A 48 CYS cc_start: 0.8050 (m) cc_final: 0.7838 (t) REVERT: A 50 MET cc_start: 0.7607 (ptp) cc_final: 0.7347 (ppp) REVERT: A 74 LEU cc_start: 0.8772 (tp) cc_final: 0.8453 (tt) REVERT: A 109 MET cc_start: 0.6614 (mmt) cc_final: 0.6338 (mmp) REVERT: A 257 MET cc_start: 0.8801 (mmt) cc_final: 0.8529 (mmt) REVERT: B 162 CYS cc_start: 0.9220 (m) cc_final: 0.8825 (m) REVERT: B 297 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 305 ASN cc_start: 0.8579 (m-40) cc_final: 0.7782 (p0) REVERT: D 50 MET cc_start: 0.8674 (mtt) cc_final: 0.8417 (mtp) REVERT: D 67 MET cc_start: 0.9314 (mmm) cc_final: 0.8641 (mmm) REVERT: D 71 MET cc_start: 0.9017 (mtm) cc_final: 0.8588 (mtm) REVERT: D 138 MET cc_start: 0.9170 (tmm) cc_final: 0.8920 (tmm) REVERT: D 142 MET cc_start: 0.8111 (ptt) cc_final: 0.6860 (ppp) REVERT: E 109 MET cc_start: 0.7604 (tpp) cc_final: 0.6780 (mtt) REVERT: E 141 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: E 289 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8818 (mm-30) REVERT: E 297 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7203 (tm-30) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.1073 time to fit residues: 19.1184 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN A 13 ASN A 151 HIS D 269 ASN D 327 ASN E 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.043502 restraints weight = 80087.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.044779 restraints weight = 43229.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045632 restraints weight = 29177.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046190 restraints weight = 22562.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046549 restraints weight = 19181.003| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15089 Z= 0.270 Angle : 0.724 11.224 20461 Z= 0.374 Chirality : 0.044 0.276 2335 Planarity : 0.004 0.031 2510 Dihedral : 8.386 160.312 2377 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.20 % Allowed : 16.41 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1800 helix: 1.21 (0.15), residues: 1195 sheet: -0.44 (0.59), residues: 70 loop : -2.38 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 101 TYR 0.022 0.002 TYR E 347 PHE 0.014 0.002 PHE C 219 TRP 0.012 0.002 TRP D 260 HIS 0.013 0.002 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.27 (15089) covalent geometry : angle 0.72448 / 0.37 (20461) hydrogen bonds : bond 0.04772 / 3.23 ( 880) hydrogen bonds : angle 4.20651 / 2.95 ( 2520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 ASN cc_start: 0.6878 (OUTLIER) cc_final: 0.6019 (p0) REVERT: C 162 CYS cc_start: 0.9230 (m) cc_final: 0.8681 (t) REVERT: C 271 MET cc_start: 0.9385 (mmm) cc_final: 0.9062 (tpp) REVERT: A 1 MET cc_start: 0.6754 (pmm) cc_final: 0.6149 (ptm) REVERT: A 48 CYS cc_start: 0.8075 (m) cc_final: 0.7775 (t) REVERT: A 109 MET cc_start: 0.6648 (mmt) cc_final: 0.6369 (mmp) REVERT: A 281 MET cc_start: 0.8254 (tpp) cc_final: 0.7973 (tpt) REVERT: B 67 MET cc_start: 0.8861 (mmm) cc_final: 0.8597 (mmm) REVERT: B 162 CYS cc_start: 0.9289 (m) cc_final: 0.8860 (m) REVERT: B 297 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8143 (tm-30) REVERT: D 50 MET cc_start: 0.8762 (mtt) cc_final: 0.8499 (mtm) REVERT: D 67 MET cc_start: 0.9400 (mmm) cc_final: 0.8937 (mmm) REVERT: D 71 MET cc_start: 0.9065 (mtm) cc_final: 0.8637 (mtm) REVERT: D 138 MET cc_start: 0.9270 (tmm) cc_final: 0.9052 (tmm) REVERT: D 142 MET cc_start: 0.8497 (ptt) cc_final: 0.7356 (ppp) REVERT: E 1 MET cc_start: 0.4638 (ptt) cc_final: 0.4405 (ptp) REVERT: E 138 MET cc_start: 0.9206 (mmm) cc_final: 0.8865 (mmm) REVERT: E 141 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: E 297 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7110 (tm-30) outliers start: 18 outliers final: 14 residues processed: 113 average time/residue: 0.1023 time to fit residues: 17.8730 Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 45 optimal weight: 40.0000 chunk 119 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.046718 restraints weight = 79660.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047981 restraints weight = 44413.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048803 restraints weight = 30368.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.049368 restraints weight = 23774.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049660 restraints weight = 20218.286| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15089 Z= 0.124 Angle : 0.602 11.521 20461 Z= 0.300 Chirality : 0.039 0.246 2335 Planarity : 0.003 0.030 2510 Dihedral : 8.048 160.564 2377 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.00 % Allowed : 17.28 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1800 helix: 1.39 (0.15), residues: 1225 sheet: -0.28 (0.59), residues: 70 loop : -2.36 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.008 0.001 TYR C 288 PHE 0.009 0.001 PHE C 219 TRP 0.002 0.001 TRP B 260 HIS 0.012 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15089) covalent geometry : angle 0.60246 / 0.30 (20461) hydrogen bonds : bond 0.03331 / 2.26 ( 880) hydrogen bonds : angle 3.64206 / 2.54 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.62 seconds wall clock time: 43 minutes 31.83 seconds (2611.83 seconds total)