Starting phenix.real_space_refine on Sat Aug 23 21:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuo_35728/08_2025/8iuo_35728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuo_35728/08_2025/8iuo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2025/8iuo_35728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2025/8iuo_35728.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2025/8iuo_35728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2025/8iuo_35728.cif" } 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-2.0-5787/lib/python3.9/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: 3.73, per 1000 atoms: 0.25 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: 1.13 Conformation dependent library (CDL) restraints added in 724.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.51 Time building geometry restraints manager: 1.60 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: 8937 34.98 - 69.96: 266 69.96 - 104.94: 15 104.94 - 139.92: 3 139.92 - 174.89: 1 Dihedral angle restraints: 9222 sinusoidal: 4032 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 9219 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: 8.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.840 Find NCS groups from input model: 0.230 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 16.368 174.894 5912 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 aren 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 covalent geometry : bond 0.00754 (15089) covalent geometry : angle 0.73764 (20461) hydrogen bonds : bond 0.13710 ( 880) hydrogen bonds : angle 4.77197 ( 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 : 0.580 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: 0.7409 (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: 0.5087 (m-70) outliers start: 33 outliers final: 9 residues processed: 234 average time/residue: 0.1557 time to fit residues: 50.2813 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 : 0.396 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.064163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049624 restraints weight = 78679.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.051038 restraints weight = 43002.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051988 restraints weight = 28887.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052635 restraints weight = 22174.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052957 restraints weight = 18555.954| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2581 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= 0.156 Angle : 0.595 8.890 20461 Z= 0.314 Chirality : 0.041 0.246 2335 Planarity : 0.004 0.036 2510 Dihedral : 11.651 159.287 2533 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.46 % Allowed : 9.24 % Favored : 89.30 % 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 aren not related in a simple way. whole: -0.57 (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 0.006 0.000 ARG D 84 TYR 0.012 0.001 TYR C 88 PHE 0.010 0.001 PHE E 213 TRP 0.004 0.001 TRP E 260 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00322 (15089) covalent geometry : angle 0.59450 (20461) hydrogen bonds : bond 0.03623 ( 880) hydrogen bonds : angle 3.77685 ( 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 : 0.577 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: 0.8915 (mtp) cc_final: 0.8587 (mtp) REVERT: C 105 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.5993 (p0) REVERT: C 271 MET cc_start: 0.9301 (mmm) cc_final: 0.8534 (mtp) REVERT: A 109 MET cc_start: 0.6711 (mmt) cc_final: 0.6342 (mmp) REVERT: A 194 MET cc_start: 0.8042 (mtm) cc_final: 0.7732 (mtm) REVERT: B 50 MET cc_start: 0.8983 (mtp) cc_final: 0.8419 (ttm) REVERT: B 271 MET cc_start: 0.8461 (mtp) cc_final: 0.8134 (mtp) REVERT: B 297 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 305 ASN cc_start: 0.7957 (m-40) cc_final: 0.7472 (p0) REVERT: D 50 MET cc_start: 0.8735 (mtt) cc_final: 0.8405 (mtm) REVERT: D 67 MET cc_start: 0.9360 (mmm) cc_final: 0.8617 (mmm) REVERT: D 71 MET cc_start: 0.9062 (mtm) cc_final: 0.8533 (mtm) REVERT: D 158 MET cc_start: 0.8746 (mmt) cc_final: 0.7835 (mmt) REVERT: D 162 CYS cc_start: 0.9106 (m) cc_final: 0.8905 (m) REVERT: D 263 LEU cc_start: 0.8939 (tp) cc_final: 0.8701 (tt) REVERT: E 9 ASN cc_start: 0.8601 (t0) cc_final: 0.8274 (t0) REVERT: E 67 MET cc_start: 0.8556 (mmm) cc_final: 0.8260 (mmt) REVERT: E 286 GLU cc_start: 0.8608 (tt0) cc_final: 0.8176 (tm-30) REVERT: E 289 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8922 (mm-30) REVERT: E 297 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7049 (tm-30) outliers start: 22 outliers final: 9 residues processed: 153 average time/residue: 0.1421 time to fit residues: 31.2369 Evaluate side-chains 122 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER 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: 9.9990 chunk 129 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 33 optimal weight: 0.0000 chunk 150 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 230 GLN A 9 ASN D 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048935 restraints weight = 79110.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050355 restraints weight = 42991.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.051305 restraints weight = 28786.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051922 restraints weight = 21998.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.052368 restraints weight = 18422.670| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15089 Z= 0.121 Angle : 0.542 8.548 20461 Z= 0.283 Chirality : 0.039 0.248 2335 Planarity : 0.003 0.032 2510 Dihedral : 11.491 160.666 2518 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.40 % Allowed : 11.83 % Favored : 86.78 % 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 aren not related in a simple way. whole: 0.17 (0.21), residues: 1800 helix: 1.36 (0.15), residues: 1175 sheet: -1.66 (0.53), residues: 70 loop : -2.46 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 84 TYR 0.009 0.001 TYR E 347 PHE 0.026 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 covalent geometry : bond 0.00256 (15089) covalent geometry : angle 0.54236 (20461) hydrogen bonds : bond 0.03373 ( 880) hydrogen bonds : angle 3.51412 ( 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 142 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.584 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 50 MET cc_start: 0.8910 (mtp) cc_final: 0.8573 (mtp) REVERT: A 74 LEU cc_start: 0.8675 (tp) cc_final: 0.8308 (tt) REVERT: A 109 MET cc_start: 0.6740 (mmt) cc_final: 0.6513 (mmp) REVERT: A 281 MET cc_start: 0.8055 (mmm) cc_final: 0.7708 (tpt) REVERT: B 71 MET cc_start: 0.9209 (mtm) cc_final: 0.8871 (mtm) REVERT: B 297 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7295 (tm-30) REVERT: B 305 ASN cc_start: 0.8167 (m-40) cc_final: 0.7638 (p0) REVERT: D 50 MET cc_start: 0.8739 (mtt) cc_final: 0.8442 (mtm) REVERT: D 67 MET cc_start: 0.9384 (mmm) cc_final: 0.8612 (mmm) REVERT: D 71 MET cc_start: 0.9051 (mtm) cc_final: 0.8544 (mtm) REVERT: D 162 CYS cc_start: 0.9129 (m) cc_final: 0.8916 (m) REVERT: E 9 ASN cc_start: 0.8660 (t0) cc_final: 0.8347 (t0) REVERT: E 67 MET cc_start: 0.8578 (mmm) cc_final: 0.8300 (mmt) REVERT: E 289 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8888 (mm-30) REVERT: E 297 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7004 (tm-30) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.1272 time to fit residues: 26.1852 Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.0570 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS D 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046794 restraints weight = 78812.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.048137 restraints weight = 42929.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049045 restraints weight = 28945.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049656 restraints weight = 22312.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049983 restraints weight = 18737.229| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15089 Z= 0.155 Angle : 0.570 9.586 20461 Z= 0.296 Chirality : 0.040 0.255 2335 Planarity : 0.003 0.032 2510 Dihedral : 11.376 159.430 2517 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.66 % Allowed : 13.02 % Favored : 85.32 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1800 helix: 1.41 (0.15), residues: 1205 sheet: -1.09 (0.55), residues: 70 loop : -2.49 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.011 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 B 225 Details of bonding type rmsd covalent geometry : bond 0.00335 (15089) covalent geometry : angle 0.56973 (20461) hydrogen bonds : bond 0.03598 ( 880) hydrogen bonds : angle 3.61502 ( 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 135 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8960 (mtp) cc_final: 0.8614 (mtp) REVERT: C 105 ASN cc_start: 0.6629 (OUTLIER) cc_final: 0.5753 (p0) REVERT: A 109 MET cc_start: 0.6670 (mmt) cc_final: 0.6355 (mmp) REVERT: A 194 MET cc_start: 0.8017 (mtm) cc_final: 0.7799 (mtt) REVERT: A 281 MET cc_start: 0.8019 (mmm) cc_final: 0.7758 (tpt) REVERT: B 162 CYS cc_start: 0.9321 (m) cc_final: 0.8970 (m) REVERT: B 297 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 305 ASN cc_start: 0.8483 (m-40) cc_final: 0.7676 (p0) REVERT: D 50 MET cc_start: 0.8803 (mtt) cc_final: 0.8518 (mtm) REVERT: D 67 MET cc_start: 0.9433 (mmm) cc_final: 0.8709 (mmm) REVERT: D 71 MET cc_start: 0.9112 (mtm) cc_final: 0.8552 (mtm) REVERT: D 158 MET cc_start: 0.8726 (mmt) cc_final: 0.8015 (mmp) REVERT: D 162 CYS cc_start: 0.9169 (m) cc_final: 0.8918 (m) REVERT: E 138 MET cc_start: 0.9250 (mmm) cc_final: 0.9043 (mmm) REVERT: E 221 ASP cc_start: 0.9113 (m-30) cc_final: 0.8878 (t0) REVERT: E 282 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8166 (tm-30) REVERT: E 289 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8938 (mm-30) REVERT: E 297 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7192 (tm-30) outliers start: 25 outliers final: 14 residues processed: 130 average time/residue: 0.1147 time to fit residues: 22.8708 Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 141 GLU 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 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 129 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.046871 restraints weight = 79179.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048220 restraints weight = 43595.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049120 restraints weight = 29571.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049732 restraints weight = 22831.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050064 restraints weight = 19255.805| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15089 Z= 0.124 Angle : 0.529 8.673 20461 Z= 0.276 Chirality : 0.039 0.248 2335 Planarity : 0.003 0.034 2510 Dihedral : 11.272 159.685 2517 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.93 % Allowed : 14.49 % Favored : 84.58 % 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 aren not related in a simple way. whole: 0.65 (0.21), residues: 1800 helix: 1.68 (0.15), residues: 1165 sheet: -0.66 (0.57), residues: 70 loop : -2.19 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 101 TYR 0.010 0.001 TYR E 347 PHE 0.013 0.001 PHE B 223 TRP 0.002 0.001 TRP E 260 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00265 (15089) covalent geometry : angle 0.52935 (20461) hydrogen bonds : bond 0.03248 ( 880) hydrogen bonds : angle 3.47098 ( 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 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASN cc_start: 0.8707 (t0) cc_final: 0.8398 (t0) REVERT: C 50 MET cc_start: 0.8964 (mtp) cc_final: 0.8604 (mtp) REVERT: C 105 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.5860 (p0) REVERT: A 48 CYS cc_start: 0.8107 (m) cc_final: 0.7662 (t) REVERT: A 74 LEU cc_start: 0.8733 (tp) cc_final: 0.8375 (tt) REVERT: A 109 MET cc_start: 0.6680 (mmt) cc_final: 0.6367 (mmp) REVERT: B 71 MET cc_start: 0.9261 (mtm) cc_final: 0.8993 (mtm) REVERT: B 162 CYS cc_start: 0.9322 (m) cc_final: 0.8944 (m) REVERT: B 297 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 305 ASN cc_start: 0.8563 (m-40) cc_final: 0.7781 (p0) REVERT: D 50 MET cc_start: 0.8770 (mtt) cc_final: 0.8486 (mtm) REVERT: D 67 MET cc_start: 0.9409 (mmm) cc_final: 0.8691 (mmm) REVERT: D 71 MET cc_start: 0.9099 (mtm) cc_final: 0.8554 (mtm) REVERT: D 109 MET cc_start: 0.7480 (tpt) cc_final: 0.7279 (tpt) REVERT: D 138 MET cc_start: 0.9176 (tpp) cc_final: 0.8941 (tmm) REVERT: D 162 CYS cc_start: 0.9182 (m) cc_final: 0.8934 (m) REVERT: E 289 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8934 (mm-30) REVERT: E 297 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7272 (tm-30) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.1189 time to fit residues: 22.5974 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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: 0.0000 chunk 6 optimal weight: 0.3980 chunk 143 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050253 restraints weight = 78706.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051557 restraints weight = 44191.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052448 restraints weight = 30248.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053036 restraints weight = 23462.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053308 restraints weight = 19790.777| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15089 Z= 0.092 Angle : 0.520 10.701 20461 Z= 0.264 Chirality : 0.037 0.233 2335 Planarity : 0.003 0.029 2510 Dihedral : 11.234 159.678 2517 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.86 % Allowed : 15.15 % 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 aren not related in a simple way. whole: 0.82 (0.21), residues: 1800 helix: 1.79 (0.15), residues: 1165 sheet: -0.46 (0.57), residues: 70 loop : -2.09 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.007 0.001 TYR E 135 PHE 0.011 0.001 PHE B 223 TRP 0.003 0.001 TRP B 260 HIS 0.003 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00185 (15089) covalent geometry : angle 0.51952 (20461) hydrogen bonds : bond 0.02761 ( 880) hydrogen bonds : angle 3.24550 ( 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 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8847 (mtp) cc_final: 0.8494 (mtp) REVERT: A 48 CYS cc_start: 0.8075 (m) cc_final: 0.7713 (t) REVERT: A 50 MET cc_start: 0.7706 (ptp) cc_final: 0.7458 (ppp) REVERT: A 109 MET cc_start: 0.6660 (mmt) cc_final: 0.6387 (mmp) REVERT: A 194 MET cc_start: 0.7533 (mtt) cc_final: 0.7282 (mtm) REVERT: A 257 MET cc_start: 0.8541 (mmt) cc_final: 0.8205 (mmt) REVERT: A 271 MET cc_start: 0.7944 (tpp) cc_final: 0.7736 (tpp) REVERT: A 281 MET cc_start: 0.8077 (tpp) cc_final: 0.7817 (tpt) REVERT: B 162 CYS cc_start: 0.9197 (m) cc_final: 0.8875 (m) REVERT: B 271 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7293 (mtp) REVERT: B 297 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 305 ASN cc_start: 0.8404 (m-40) cc_final: 0.7719 (p0) REVERT: D 50 MET cc_start: 0.8634 (mtt) cc_final: 0.8349 (mtm) REVERT: D 67 MET cc_start: 0.9255 (mmm) cc_final: 0.8513 (mmm) REVERT: D 71 MET cc_start: 0.8990 (mtm) cc_final: 0.8540 (mtm) REVERT: D 158 MET cc_start: 0.8534 (mmt) cc_final: 0.7797 (mmp) REVERT: E 67 MET cc_start: 0.8510 (mmm) cc_final: 0.8255 (mmt) REVERT: E 289 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8792 (mm-30) REVERT: E 297 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7116 (tm-30) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.1306 time to fit residues: 24.6277 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 : 0.588 ------------------------------------------------------------------------------- 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 34 ASP 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 1 MET 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: 0.0010 chunk 162 optimal weight: 0.0170 chunk 174 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 55 optimal weight: 0.0010 chunk 92 optimal weight: 6.9990 overall best weight: 1.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.062819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048691 restraints weight = 78667.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049970 restraints weight = 44150.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050869 restraints weight = 30139.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051444 restraints weight = 23435.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051707 restraints weight = 19868.210| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4643 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= 0.105 Angle : 0.536 10.283 20461 Z= 0.272 Chirality : 0.038 0.240 2335 Planarity : 0.003 0.027 2510 Dihedral : 11.256 159.100 2517 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.06 % Allowed : 15.95 % Favored : 82.99 % 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 aren not related in a simple way. whole: 0.95 (0.21), residues: 1800 helix: 1.90 (0.15), residues: 1160 sheet: -0.27 (0.59), residues: 70 loop : -2.06 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.007 0.001 TYR E 347 PHE 0.014 0.001 PHE E 223 TRP 0.002 0.000 TRP B 260 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00227 (15089) covalent geometry : angle 0.53619 (20461) hydrogen bonds : bond 0.02953 ( 880) hydrogen bonds : angle 3.28741 ( 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 121 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8916 (mtp) cc_final: 0.8532 (mtp) REVERT: C 105 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.5649 (p0) REVERT: A 48 CYS cc_start: 0.8046 (m) cc_final: 0.7681 (t) REVERT: A 50 MET cc_start: 0.7710 (ptp) cc_final: 0.7477 (ppp) REVERT: A 74 LEU cc_start: 0.8701 (tp) cc_final: 0.8396 (tt) REVERT: A 109 MET cc_start: 0.6691 (mmt) cc_final: 0.6410 (mmp) REVERT: A 194 MET cc_start: 0.7730 (mtt) cc_final: 0.7423 (mtm) REVERT: A 257 MET cc_start: 0.8665 (mmt) cc_final: 0.8370 (mmt) REVERT: A 281 MET cc_start: 0.8177 (tpp) cc_final: 0.7912 (tpt) REVERT: B 162 CYS cc_start: 0.9244 (m) cc_final: 0.8889 (m) REVERT: B 271 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7424 (mtp) REVERT: B 297 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7268 (tm-30) REVERT: B 305 ASN cc_start: 0.8465 (m-40) cc_final: 0.7693 (p0) REVERT: D 50 MET cc_start: 0.8663 (mtt) cc_final: 0.8409 (mtp) REVERT: D 67 MET cc_start: 0.9306 (mmm) cc_final: 0.8540 (mmm) REVERT: D 71 MET cc_start: 0.9046 (mtm) cc_final: 0.8601 (mtm) REVERT: D 138 MET cc_start: 0.9230 (tmm) cc_final: 0.8975 (tmm) REVERT: D 142 MET cc_start: 0.8156 (ptt) cc_final: 0.6461 (ppp) REVERT: E 289 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8821 (mm-30) REVERT: E 297 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7121 (tm-30) outliers start: 16 outliers final: 11 residues processed: 117 average time/residue: 0.1205 time to fit residues: 21.6648 Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 271 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 0.0070 chunk 17 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.063489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049554 restraints weight = 78729.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050850 restraints weight = 44253.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.051739 restraints weight = 30252.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052298 restraints weight = 23401.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052686 restraints weight = 19862.939| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4859 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= 0.098 Angle : 0.543 11.343 20461 Z= 0.270 Chirality : 0.037 0.235 2335 Planarity : 0.003 0.027 2510 Dihedral : 11.372 159.042 2517 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.26 % Allowed : 16.15 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 1800 helix: 1.73 (0.15), residues: 1190 sheet: -0.17 (0.59), residues: 70 loop : -2.39 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 101 TYR 0.006 0.001 TYR B 288 PHE 0.011 0.001 PHE E 223 TRP 0.002 0.000 TRP B 260 HIS 0.003 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00210 (15089) covalent geometry : angle 0.54251 (20461) hydrogen bonds : bond 0.02821 ( 880) hydrogen bonds : angle 3.24823 ( 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 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8881 (mtp) cc_final: 0.8493 (mtp) REVERT: C 105 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.5692 (p0) REVERT: A 48 CYS cc_start: 0.8043 (m) cc_final: 0.7713 (t) REVERT: A 50 MET cc_start: 0.7701 (ptp) cc_final: 0.7489 (ppp) REVERT: A 74 LEU cc_start: 0.8717 (tp) cc_final: 0.8439 (tt) REVERT: A 109 MET cc_start: 0.6651 (mmt) cc_final: 0.6379 (mmp) REVERT: A 257 MET cc_start: 0.8679 (mmt) cc_final: 0.8431 (mmt) REVERT: B 162 CYS cc_start: 0.9246 (m) cc_final: 0.8904 (m) REVERT: B 297 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 305 ASN cc_start: 0.8495 (m-40) cc_final: 0.7755 (p0) REVERT: D 50 MET cc_start: 0.8634 (mtt) cc_final: 0.8356 (mtp) REVERT: D 67 MET cc_start: 0.9274 (mmm) cc_final: 0.8523 (mmm) REVERT: D 71 MET cc_start: 0.9039 (mtm) cc_final: 0.8606 (mtm) REVERT: D 138 MET cc_start: 0.9148 (tmm) cc_final: 0.8942 (tmm) REVERT: E 67 MET cc_start: 0.8574 (mmm) cc_final: 0.8364 (mmt) REVERT: E 109 MET cc_start: 0.7250 (tpp) cc_final: 0.6578 (mtt) REVERT: E 289 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8837 (mm-30) REVERT: E 297 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7109 (tm-30) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.1154 time to fit residues: 22.3997 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 : 0.471 ------------------------------------------------------------------------------- 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 B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 67 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 151 optimal weight: 0.0000 chunk 149 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN E 58 ASN E 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.046141 restraints weight = 79648.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.047382 restraints weight = 45071.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.048231 restraints weight = 31161.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048649 restraints weight = 24456.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049128 restraints weight = 21158.532| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15089 Z= 0.178 Angle : 0.628 11.283 20461 Z= 0.316 Chirality : 0.040 0.260 2335 Planarity : 0.003 0.029 2510 Dihedral : 11.342 159.397 2517 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.13 % Allowed : 16.81 % Favored : 82.06 % 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 aren not related in a simple way. whole: 0.62 (0.20), residues: 1800 helix: 1.60 (0.15), residues: 1190 sheet: -0.12 (0.60), residues: 70 loop : -2.34 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.014 0.001 TYR E 347 PHE 0.011 0.001 PHE C 219 TRP 0.006 0.001 TRP D 260 HIS 0.009 0.001 HIS E 151 Details of bonding type rmsd covalent geometry : bond 0.00390 (15089) covalent geometry : angle 0.62769 (20461) hydrogen bonds : bond 0.03731 ( 880) hydrogen bonds : angle 3.64584 ( 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 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8972 (mtp) cc_final: 0.8620 (mtp) REVERT: C 105 ASN cc_start: 0.6744 (OUTLIER) cc_final: 0.5858 (p0) REVERT: C 162 CYS cc_start: 0.9200 (m) cc_final: 0.8746 (t) REVERT: A 48 CYS cc_start: 0.8079 (m) cc_final: 0.7717 (t) REVERT: A 74 LEU cc_start: 0.8721 (tp) cc_final: 0.8444 (tt) REVERT: A 109 MET cc_start: 0.6729 (mmt) cc_final: 0.6441 (mmp) REVERT: A 257 MET cc_start: 0.8845 (mmt) cc_final: 0.8521 (mmt) REVERT: A 281 MET cc_start: 0.8262 (tpp) cc_final: 0.7963 (tpt) REVERT: B 162 CYS cc_start: 0.9287 (m) cc_final: 0.8896 (m) REVERT: B 297 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 305 ASN cc_start: 0.8788 (m-40) cc_final: 0.7836 (p0) REVERT: D 50 MET cc_start: 0.8726 (mtt) cc_final: 0.8450 (mtp) REVERT: D 67 MET cc_start: 0.9354 (mmm) cc_final: 0.8794 (mmm) REVERT: D 71 MET cc_start: 0.9067 (mtm) cc_final: 0.8583 (mtm) REVERT: D 142 MET cc_start: 0.8291 (ptt) cc_final: 0.7213 (ppp) REVERT: E 109 MET cc_start: 0.7578 (tpp) cc_final: 0.6760 (mtt) REVERT: E 141 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: E 289 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8867 (mm-30) REVERT: E 297 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7126 (tm-30) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.1211 time to fit residues: 20.9978 Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN A 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.046506 restraints weight = 80490.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047735 restraints weight = 45170.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048573 restraints weight = 31140.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049125 restraints weight = 24264.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049416 restraints weight = 20755.978| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15089 Z= 0.174 Angle : 0.631 11.358 20461 Z= 0.317 Chirality : 0.040 0.254 2335 Planarity : 0.003 0.030 2510 Dihedral : 11.409 160.852 2517 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.13 % Allowed : 16.68 % Favored : 82.19 % 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 aren not related in a simple way. whole: 0.49 (0.20), residues: 1800 helix: 1.45 (0.15), residues: 1195 sheet: 0.01 (0.60), residues: 70 loop : -2.31 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.012 0.001 TYR E 347 PHE 0.010 0.001 PHE C 219 TRP 0.004 0.001 TRP D 260 HIS 0.011 0.001 HIS E 151 Details of bonding type rmsd covalent geometry : bond 0.00382 (15089) covalent geometry : angle 0.63060 (20461) hydrogen bonds : bond 0.03715 ( 880) hydrogen bonds : angle 3.74396 ( 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 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8885 (mtp) cc_final: 0.8559 (mtp) REVERT: C 105 ASN cc_start: 0.6667 (OUTLIER) cc_final: 0.5753 (p0) REVERT: A 1 MET cc_start: 0.6867 (pmm) cc_final: 0.6199 (ptm) REVERT: A 48 CYS cc_start: 0.8095 (m) cc_final: 0.7756 (t) REVERT: A 74 LEU cc_start: 0.8701 (tp) cc_final: 0.8402 (tt) REVERT: A 109 MET cc_start: 0.6745 (mmt) cc_final: 0.6479 (mmp) REVERT: A 281 MET cc_start: 0.8117 (tpp) cc_final: 0.7850 (tpt) REVERT: B 162 CYS cc_start: 0.9193 (m) cc_final: 0.8788 (m) REVERT: B 297 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 50 MET cc_start: 0.8671 (mtt) cc_final: 0.8386 (mtm) REVERT: D 67 MET cc_start: 0.9300 (mmm) cc_final: 0.8801 (mmm) REVERT: D 71 MET cc_start: 0.8984 (mtm) cc_final: 0.8559 (mtm) REVERT: D 142 MET cc_start: 0.8327 (ptt) cc_final: 0.7340 (ppp) REVERT: E 109 MET cc_start: 0.7627 (tpp) cc_final: 0.6836 (mtt) REVERT: E 138 MET cc_start: 0.9162 (mmm) cc_final: 0.8863 (mmm) REVERT: E 141 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: E 289 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8800 (mm-30) REVERT: E 297 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7098 (tm-30) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 0.1158 time to fit residues: 20.4499 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 105 ASN 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 45 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 79 optimal weight: 0.0470 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048699 restraints weight = 78462.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049974 restraints weight = 43906.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050832 restraints weight = 30024.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051381 restraints weight = 23369.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051681 restraints weight = 19907.191| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15089 Z= 0.100 Angle : 0.582 13.166 20461 Z= 0.286 Chirality : 0.038 0.234 2335 Planarity : 0.003 0.028 2510 Dihedral : 11.439 160.309 2517 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.86 % Allowed : 17.14 % Favored : 81.99 % 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 aren not related in a simple way. whole: 0.49 (0.20), residues: 1800 helix: 1.55 (0.15), residues: 1205 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.007 0.001 TYR C 347 PHE 0.009 0.001 PHE C 219 TRP 0.003 0.001 TRP B 260 HIS 0.007 0.000 HIS E 151 Details of bonding type rmsd covalent geometry : bond 0.00211 (15089) covalent geometry : angle 0.58181 (20461) hydrogen bonds : bond 0.02975 ( 880) hydrogen bonds : angle 3.42052 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.11 seconds wall clock time: 46 minutes 37.71 seconds (2797.71 seconds total)