Starting phenix.real_space_refine on Thu Aug 6 10:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.cif" model { file = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_35728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuo_35728/08_2026/8iuo_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 3.37, per 1000 atoms: 0.23 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: 1.19 Conformation dependent library (CDL) restraints added in 604.7 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 71.5% alpha, 5.0% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.22 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: 2.35 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 18942 1.31 - 2.63: 1223 2.63 - 3.94: 212 3.94 - 5.25: 67 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=" C3' U F1014 " pdb=" O3' U F1014 " pdb=" P U F1015 " ideal model delta sigma weight residual 119.70 124.14 -4.44 1.20e+00 6.94e-01 1.37e+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: 8818 34.98 - 69.96: 241 69.96 - 104.94: 19 104.94 - 139.92: 3 139.92 - 174.89: 1 Dihedral angle restraints: 9082 sinusoidal: 3892 harmonic: 5190 Sorted by residual: dihedral pdb=" C4' U F1018 " pdb=" C3' U F1018 " pdb=" C2' U F1018 " pdb=" C1' U F1018 " ideal model delta sinusoidal sigma weight residual 36.34 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U F1004 " pdb=" C3' U F1004 " pdb=" C2' U F1004 " pdb=" C1' U F1004 " ideal model delta sinusoidal sigma weight residual 36.34 -35.59 71.93 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' U F1011 " pdb=" C3' U F1011 " pdb=" C2' U F1011 " pdb=" C1' U F1011 " ideal model delta sinusoidal sigma weight residual 36.34 -35.40 71.75 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 9079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1876 0.057 - 0.114: 380 0.114 - 0.171: 24 0.171 - 0.228: 35 0.228 - 0.285: 20 Chirality restraints: 2335 Sorted by residual: chirality pdb=" C2' U F1025 " pdb=" C3' U F1025 " pdb=" O2' U F1025 " pdb=" C1' U F1025 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' U F1004 " pdb=" C3' U F1004 " pdb=" O2' U F1004 " pdb=" C1' U F1004 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' U F1032 " pdb=" C3' U F1032 " pdb=" O2' U F1032 " pdb=" C1' U F1032 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+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: 9.410 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 15089 Z= 0.370 Angle : 0.770 6.563 20461 Z= 0.446 Chirality : 0.054 0.285 2335 Planarity : 0.004 0.046 2510 Dihedral : 16.151 174.894 5772 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.19 % Allowed : 2.79 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.18), residues: 1800 helix: -0.79 (0.13), residues: 1165 sheet: -3.72 (0.41), residues: 125 loop : -2.70 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 27 TYR 0.010 0.001 TYR C 210 PHE 0.011 0.001 PHE A 247 TRP 0.002 0.001 TRP D 260 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.37 (15089) covalent geometry : angle 0.76985 / 0.45 (20461) hydrogen bonds : bond 0.13710 / 9.19 ( 880) hydrogen bonds : angle 4.77197 / 3.52 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 MET cc_start: 0.7972 (ptp) cc_final: 0.7408 (ptm) REVERT: C 271 MET cc_start: 0.9268 (mmm) cc_final: 0.8521 (mtp) REVERT: C 315 THR cc_start: 0.8675 (m) cc_final: 0.8434 (m) REVERT: A 194 MET cc_start: 0.7853 (mtm) cc_final: 0.7582 (mtt) REVERT: B 158 MET cc_start: 0.8021 (mmm) cc_final: 0.7776 (mmm) REVERT: B 286 GLU cc_start: 0.7953 (tp30) cc_final: 0.7261 (tp30) REVERT: B 297 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 305 ASN cc_start: 0.7947 (m-40) cc_final: 0.7445 (p0) REVERT: D 50 MET cc_start: 0.8635 (mtt) cc_final: 0.8327 (mtm) REVERT: D 71 MET cc_start: 0.8935 (mtm) cc_final: 0.8705 (mtt) REVERT: D 142 MET cc_start: 0.8464 (ptp) cc_final: 0.7780 (ptp) REVERT: D 263 LEU cc_start: 0.8843 (tp) cc_final: 0.8578 (tt) REVERT: E 134 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7402 (m) REVERT: E 216 HIS cc_start: 0.5384 (OUTLIER) cc_final: 0.5088 (m-70) outliers start: 33 outliers final: 9 residues processed: 234 average time/residue: 0.1297 time to fit residues: 42.2663 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 : 0.543 ------------------------------------------------------------------------------- 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... C 100 HIS B 216 HIS D 16 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 = 0.3391 r_free = 0.3391 target = 0.064452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050011 restraints weight = 78816.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051437 restraints weight = 43029.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052400 restraints weight = 28871.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052994 restraints weight = 22116.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053458 restraints weight = 18641.243| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2521 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= 0.155 Angle : 0.667 9.076 20461 Z= 0.320 Chirality : 0.048 0.375 2335 Planarity : 0.004 0.037 2510 Dihedral : 10.884 152.957 2393 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.33 % Allowed : 9.24 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1800 helix: 0.79 (0.15), residues: 1205 sheet: -3.23 (0.37), residues: 125 loop : -2.62 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 101 TYR 0.011 0.001 TYR B 23 PHE 0.012 0.001 PHE D 111 TRP 0.004 0.001 TRP E 260 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (15089) covalent geometry : angle 0.66736 / 0.32 (20461) hydrogen bonds : bond 0.03677 / 2.47 ( 880) hydrogen bonds : angle 3.80204 / 2.69 ( 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 153 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.560 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: 0.8879 (mtp) cc_final: 0.8554 (mtp) REVERT: C 105 ASN cc_start: 0.6599 (OUTLIER) cc_final: 0.5962 (p0) REVERT: C 271 MET cc_start: 0.9305 (mmm) cc_final: 0.8518 (mtp) REVERT: A 109 MET cc_start: 0.6516 (mmt) cc_final: 0.6133 (mmp) REVERT: A 194 MET cc_start: 0.8025 (mtm) cc_final: 0.7722 (mtm) REVERT: B 50 MET cc_start: 0.8989 (mtp) cc_final: 0.8435 (ttm) REVERT: B 271 MET cc_start: 0.8449 (mtp) cc_final: 0.8071 (mtp) REVERT: B 297 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7172 (tm-30) REVERT: B 305 ASN cc_start: 0.7955 (m-40) cc_final: 0.7475 (p0) REVERT: D 50 MET cc_start: 0.8730 (mtt) cc_final: 0.8409 (mtm) REVERT: D 67 MET cc_start: 0.9364 (mmm) cc_final: 0.8608 (mmm) REVERT: D 71 MET cc_start: 0.9050 (mtm) cc_final: 0.8614 (mtm) REVERT: D 158 MET cc_start: 0.8729 (mmt) cc_final: 0.7816 (mmt) REVERT: D 263 LEU cc_start: 0.8925 (tp) cc_final: 0.8686 (tt) REVERT: E 9 ASN cc_start: 0.8595 (t0) cc_final: 0.8270 (t0) REVERT: E 67 MET cc_start: 0.8559 (mmm) cc_final: 0.8247 (mmt) REVERT: E 286 GLU cc_start: 0.8600 (tt0) cc_final: 0.8158 (tm-30) REVERT: E 289 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8920 (mm-30) REVERT: E 297 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6945 (tm-30) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.1244 time to fit residues: 26.8645 Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 240 GLU Chi-restraints excluded: chain E residue 27 ARG 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: 2.9990 chunk 14 optimal weight: 0.0470 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN C 124 GLN C 230 GLN A 9 ASN A 59 HIS D 16 GLN E 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048837 restraints weight = 79025.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.050239 restraints weight = 43019.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051183 restraints weight = 28919.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051791 restraints weight = 22165.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052267 restraints weight = 18624.272| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15089 Z= 0.130 Angle : 0.612 8.762 20461 Z= 0.292 Chirality : 0.048 0.366 2335 Planarity : 0.003 0.033 2510 Dihedral : 10.659 153.466 2378 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.46 % Allowed : 11.83 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1800 helix: 1.41 (0.15), residues: 1175 sheet: -1.57 (0.53), residues: 70 loop : -2.44 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.011 0.001 TYR D 23 PHE 0.028 0.001 PHE B 223 TRP 0.005 0.001 TRP E 260 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15089) covalent geometry : angle 0.61218 / 0.29 (20461) hydrogen bonds : bond 0.03329 / 2.25 ( 880) hydrogen bonds : angle 3.53687 / 2.47 ( 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: 22 poor density : 120 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASN cc_start: 0.8671 (t0) cc_final: 0.8268 (t0) REVERT: C 50 MET cc_start: 0.8904 (mtp) cc_final: 0.8575 (mtp) REVERT: C 271 MET cc_start: 0.9355 (mmm) cc_final: 0.9149 (mmp) REVERT: A 109 MET cc_start: 0.6683 (mmt) cc_final: 0.6403 (mmp) REVERT: A 194 MET cc_start: 0.8014 (mtm) cc_final: 0.7777 (mtt) REVERT: A 281 MET cc_start: 0.8063 (mmm) cc_final: 0.7670 (tpt) REVERT: B 71 MET cc_start: 0.9221 (mtm) cc_final: 0.8914 (mtm) REVERT: B 297 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 305 ASN cc_start: 0.8217 (m-40) cc_final: 0.7569 (p0) REVERT: D 50 MET cc_start: 0.8755 (mtt) cc_final: 0.8463 (mtm) REVERT: D 67 MET cc_start: 0.9385 (mmm) cc_final: 0.8631 (mmm) REVERT: D 71 MET cc_start: 0.9026 (mtm) cc_final: 0.8432 (mtm) REVERT: D 138 MET cc_start: 0.9034 (tpp) cc_final: 0.8711 (tmm) REVERT: E 9 ASN cc_start: 0.8674 (t0) cc_final: 0.8428 (t0) REVERT: E 282 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 289 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8888 (mm-30) REVERT: E 297 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7036 (tm-30) outliers start: 22 outliers final: 9 residues processed: 139 average time/residue: 0.1009 time to fit residues: 21.2189 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 B residue 48 CYS Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.047980 restraints weight = 78807.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049373 restraints weight = 43040.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050330 restraints weight = 28966.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050947 restraints weight = 22113.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051296 restraints weight = 18639.143| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15089 Z= 0.131 Angle : 0.617 9.653 20461 Z= 0.291 Chirality : 0.048 0.380 2335 Planarity : 0.003 0.032 2510 Dihedral : 10.571 152.531 2377 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.46 % Allowed : 13.29 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1800 helix: 1.56 (0.15), residues: 1175 sheet: -1.10 (0.57), residues: 70 loop : -2.28 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.009 0.001 TYR E 337 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/Z covalent geometry : bond 0.00281 / 0.13 (15089) covalent geometry : angle 0.61740 / 0.29 (20461) hydrogen bonds : bond 0.03323 / 2.24 ( 880) hydrogen bonds : angle 3.50970 / 2.44 ( 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 130 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8912 (mtp) cc_final: 0.8570 (mtp) REVERT: C 105 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.5786 (p0) REVERT: C 142 MET cc_start: 0.8058 (ttp) cc_final: 0.6978 (mpp) REVERT: C 271 MET cc_start: 0.9371 (mmm) cc_final: 0.8978 (mmp) REVERT: A 109 MET cc_start: 0.6691 (mmt) cc_final: 0.6390 (mmp) REVERT: A 194 MET cc_start: 0.8062 (mtm) cc_final: 0.7793 (mtt) REVERT: A 281 MET cc_start: 0.8069 (mmm) cc_final: 0.7755 (tpt) REVERT: B 297 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 305 ASN cc_start: 0.8387 (m-40) cc_final: 0.7681 (p0) REVERT: D 50 MET cc_start: 0.8776 (mtt) cc_final: 0.8495 (mtm) REVERT: D 67 MET cc_start: 0.9396 (mmm) cc_final: 0.8638 (mmm) REVERT: D 71 MET cc_start: 0.9090 (mtm) cc_final: 0.8517 (mtm) REVERT: D 142 MET cc_start: 0.8134 (pmm) cc_final: 0.7923 (pmm) REVERT: E 138 MET cc_start: 0.9251 (mmm) cc_final: 0.9035 (mmm) REVERT: E 282 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8142 (tm-30) REVERT: E 289 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8883 (mm-30) REVERT: E 297 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7122 (tm-30) outliers start: 22 outliers final: 13 residues processed: 127 average time/residue: 0.1049 time to fit residues: 20.4704 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 239 VAL 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 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 129 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 16 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.049050 restraints weight = 78363.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050455 restraints weight = 42822.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051402 restraints weight = 28762.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052028 restraints weight = 22074.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052453 restraints weight = 18529.804| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15089 Z= 0.097 Angle : 0.587 10.909 20461 Z= 0.272 Chirality : 0.047 0.356 2335 Planarity : 0.003 0.031 2510 Dihedral : 10.474 154.291 2377 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.86 % Allowed : 14.22 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1800 helix: 1.70 (0.15), residues: 1175 sheet: -0.77 (0.57), residues: 70 loop : -2.11 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.007 0.001 TYR B 135 PHE 0.013 0.001 PHE B 223 TRP 0.002 0.001 TRP D 260 HIS 0.004 0.000 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (15089) covalent geometry : angle 0.58656 / 0.27 (20461) hydrogen bonds : bond 0.02946 / 1.99 ( 880) hydrogen bonds : angle 3.30115 / 2.29 ( 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 130 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8937 (mtp) cc_final: 0.8570 (mtp) REVERT: C 105 ASN cc_start: 0.6624 (OUTLIER) cc_final: 0.5800 (p0) REVERT: C 271 MET cc_start: 0.9371 (mmm) cc_final: 0.9015 (mmp) REVERT: A 48 CYS cc_start: 0.8072 (m) cc_final: 0.7621 (t) REVERT: A 109 MET cc_start: 0.6664 (mmt) cc_final: 0.6371 (mmp) REVERT: A 271 MET cc_start: 0.8460 (tpp) cc_final: 0.8238 (tpp) REVERT: A 281 MET cc_start: 0.7950 (mmm) cc_final: 0.7701 (tpt) REVERT: B 71 MET cc_start: 0.9227 (mtm) cc_final: 0.8917 (mtm) REVERT: B 162 CYS cc_start: 0.9348 (m) cc_final: 0.9002 (m) REVERT: B 297 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 305 ASN cc_start: 0.8440 (m-40) cc_final: 0.7700 (p0) REVERT: D 50 MET cc_start: 0.8749 (mtt) cc_final: 0.8457 (mtm) REVERT: D 67 MET cc_start: 0.9380 (mmm) cc_final: 0.8599 (mmm) REVERT: D 71 MET cc_start: 0.9113 (mtm) cc_final: 0.8597 (mtm) REVERT: D 142 MET cc_start: 0.7980 (pmm) cc_final: 0.7727 (pmm) REVERT: E 221 ASP cc_start: 0.9065 (m-30) cc_final: 0.8862 (t0) REVERT: E 282 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 289 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8923 (mm-30) REVERT: E 297 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7143 (tm-30) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 0.1121 time to fit residues: 22.0365 Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 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 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: 5.9990 chunk 6 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 177 optimal weight: 0.0770 chunk 168 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS ** 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 = 0.3358 r_free = 0.3358 target = 0.063140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048508 restraints weight = 78659.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.049874 restraints weight = 43622.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050803 restraints weight = 29640.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051416 restraints weight = 22889.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051764 restraints weight = 19347.473| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15089 Z= 0.106 Angle : 0.592 8.754 20461 Z= 0.277 Chirality : 0.047 0.368 2335 Planarity : 0.003 0.029 2510 Dihedral : 10.435 154.352 2377 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.20 % Allowed : 14.55 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1800 helix: 1.84 (0.15), residues: 1165 sheet: -0.51 (0.58), residues: 70 loop : -2.07 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.008 0.001 TYR E 347 PHE 0.011 0.001 PHE B 223 TRP 0.002 0.000 TRP B 260 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (15089) covalent geometry : angle 0.59188 / 0.28 (20461) hydrogen bonds : bond 0.03020 / 2.04 ( 880) hydrogen bonds : angle 3.30936 / 2.30 ( 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: 18 poor density : 111 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8930 (mtp) cc_final: 0.8568 (mtp) REVERT: C 105 ASN cc_start: 0.6643 (OUTLIER) cc_final: 0.5805 (p0) REVERT: C 142 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7624 (tmm) REVERT: C 271 MET cc_start: 0.9378 (mmm) cc_final: 0.9013 (mmp) REVERT: A 48 CYS cc_start: 0.8077 (m) cc_final: 0.7671 (t) REVERT: A 109 MET cc_start: 0.6691 (mmt) cc_final: 0.6395 (mmp) REVERT: A 257 MET cc_start: 0.8639 (mmt) cc_final: 0.8278 (mmt) REVERT: A 281 MET cc_start: 0.7911 (mmm) cc_final: 0.7673 (tpt) REVERT: B 162 CYS cc_start: 0.9302 (m) cc_final: 0.8937 (m) REVERT: B 271 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7486 (mtp) REVERT: B 297 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 305 ASN cc_start: 0.8385 (m-40) cc_final: 0.7679 (p0) REVERT: D 50 MET cc_start: 0.8722 (mtt) cc_final: 0.8460 (mtp) REVERT: D 67 MET cc_start: 0.9346 (mmm) cc_final: 0.8574 (mmm) REVERT: D 71 MET cc_start: 0.9075 (mtm) cc_final: 0.8553 (mtm) REVERT: D 142 MET cc_start: 0.7948 (pmm) cc_final: 0.7670 (pmm) REVERT: E 289 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8863 (mm-30) REVERT: E 297 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7154 (tm-30) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.1060 time to fit residues: 20.1446 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 142 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 A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 4 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 0.0020 chunk 132 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047300 restraints weight = 77940.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048678 restraints weight = 42436.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049609 restraints weight = 28532.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050246 restraints weight = 21941.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050623 restraints weight = 18403.856| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15089 Z= 0.132 Angle : 0.622 10.129 20461 Z= 0.291 Chirality : 0.048 0.382 2335 Planarity : 0.003 0.029 2510 Dihedral : 10.455 152.653 2377 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.20 % Allowed : 15.68 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1800 helix: 1.88 (0.15), residues: 1160 sheet: -0.39 (0.58), residues: 70 loop : -2.02 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.009 0.001 TYR E 337 PHE 0.011 0.001 PHE E 226 TRP 0.002 0.001 TRP E 260 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15089) covalent geometry : angle 0.62222 / 0.29 (20461) hydrogen bonds : bond 0.03307 / 2.23 ( 880) hydrogen bonds : angle 3.43162 / 2.38 ( 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 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8975 (mtp) cc_final: 0.8612 (mtp) REVERT: C 105 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.5814 (p0) REVERT: C 142 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7508 (tmm) REVERT: C 271 MET cc_start: 0.9381 (mmm) cc_final: 0.9178 (mmp) REVERT: A 48 CYS cc_start: 0.8071 (m) cc_final: 0.7671 (t) REVERT: A 50 MET cc_start: 0.7700 (ptp) cc_final: 0.7482 (ppp) REVERT: A 109 MET cc_start: 0.6656 (mmt) cc_final: 0.6364 (mmp) REVERT: A 257 MET cc_start: 0.8797 (mmt) cc_final: 0.8467 (mmt) REVERT: B 162 CYS cc_start: 0.9335 (m) cc_final: 0.8955 (m) REVERT: B 271 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7574 (mtp) REVERT: B 297 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 305 ASN cc_start: 0.8575 (m-40) cc_final: 0.7717 (p0) REVERT: D 50 MET cc_start: 0.8752 (mtt) cc_final: 0.8493 (mtp) REVERT: D 67 MET cc_start: 0.9390 (mmm) cc_final: 0.8671 (mmm) REVERT: D 71 MET cc_start: 0.9094 (mtm) cc_final: 0.8532 (mtm) REVERT: D 142 MET cc_start: 0.8002 (pmm) cc_final: 0.7696 (pmm) REVERT: E 289 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8891 (mm-30) REVERT: E 297 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7236 (tm-30) outliers start: 18 outliers final: 13 residues processed: 115 average time/residue: 0.0918 time to fit residues: 16.5076 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 156 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.048895 restraints weight = 78258.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050202 restraints weight = 44037.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051106 restraints weight = 30179.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051694 restraints weight = 23375.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052083 restraints weight = 19778.561| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15089 Z= 0.109 Angle : 0.620 11.500 20461 Z= 0.285 Chirality : 0.047 0.363 2335 Planarity : 0.003 0.028 2510 Dihedral : 10.427 153.821 2377 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.26 % Allowed : 15.68 % Favored : 83.06 % 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 are not related in a simple way. whole: 0.98 (0.21), residues: 1800 helix: 1.90 (0.15), residues: 1160 sheet: -0.31 (0.59), residues: 70 loop : -1.97 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.007 0.001 TYR E 347 PHE 0.011 0.001 PHE D 111 TRP 0.002 0.000 TRP B 260 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15089) covalent geometry : angle 0.62000 / 0.28 (20461) hydrogen bonds : bond 0.03009 / 2.03 ( 880) hydrogen bonds : angle 3.34043 / 2.31 ( 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 128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8908 (mtp) cc_final: 0.8526 (mtp) REVERT: C 105 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.5735 (p0) REVERT: C 142 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7475 (tmm) REVERT: C 271 MET cc_start: 0.9381 (mmm) cc_final: 0.9173 (mmp) REVERT: A 48 CYS cc_start: 0.8074 (m) cc_final: 0.7722 (t) REVERT: A 50 MET cc_start: 0.7698 (ptp) cc_final: 0.7480 (ppp) REVERT: A 109 MET cc_start: 0.6643 (mmt) cc_final: 0.6378 (mmp) REVERT: A 257 MET cc_start: 0.8742 (mmt) cc_final: 0.8460 (mmt) REVERT: A 281 MET cc_start: 0.8153 (tpp) cc_final: 0.7859 (tpt) REVERT: B 162 CYS cc_start: 0.9280 (m) cc_final: 0.8924 (m) REVERT: B 271 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7483 (mtp) REVERT: B 297 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 305 ASN cc_start: 0.8519 (m-40) cc_final: 0.7765 (p0) REVERT: D 50 MET cc_start: 0.8662 (mtt) cc_final: 0.8387 (mtp) REVERT: D 67 MET cc_start: 0.9327 (mmm) cc_final: 0.8616 (mmm) REVERT: D 71 MET cc_start: 0.9046 (mtm) cc_final: 0.8558 (mtm) REVERT: D 142 MET cc_start: 0.7833 (pmm) cc_final: 0.7533 (pmm) REVERT: E 109 MET cc_start: 0.7351 (tpp) cc_final: 0.6590 (mtt) REVERT: E 289 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8845 (mm-30) REVERT: E 297 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7202 (tm-30) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.1077 time to fit residues: 20.6720 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 : 0.563 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 67 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN B 249 ASN E 58 ASN E 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.060739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046456 restraints weight = 80222.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047697 restraints weight = 45142.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.048546 restraints weight = 31096.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049102 restraints weight = 24310.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049397 restraints weight = 20729.750| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15089 Z= 0.198 Angle : 0.712 12.465 20461 Z= 0.335 Chirality : 0.050 0.409 2335 Planarity : 0.003 0.030 2510 Dihedral : 10.562 150.337 2377 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.26 % Allowed : 16.35 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1800 helix: 1.70 (0.15), residues: 1160 sheet: -0.26 (0.59), residues: 70 loop : -1.94 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.015 0.001 TYR E 347 PHE 0.010 0.001 PHE C 219 TRP 0.005 0.001 TRP D 260 HIS 0.009 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (15089) covalent geometry : angle 0.71190 / 0.33 (20461) hydrogen bonds : bond 0.03928 / 2.65 ( 880) hydrogen bonds : angle 3.77443 / 2.63 ( 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 118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8907 (mtp) cc_final: 0.8581 (mtp) REVERT: C 105 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.5849 (p0) REVERT: C 142 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7468 (tmm) REVERT: C 162 CYS cc_start: 0.9187 (m) cc_final: 0.8522 (t) REVERT: C 271 MET cc_start: 0.9383 (mmm) cc_final: 0.8941 (tpp) REVERT: A 48 CYS cc_start: 0.8096 (m) cc_final: 0.7757 (t) REVERT: A 74 LEU cc_start: 0.8728 (tp) cc_final: 0.8426 (tt) REVERT: A 109 MET cc_start: 0.6707 (mmt) cc_final: 0.6417 (mmp) REVERT: A 194 MET cc_start: 0.7917 (mtm) cc_final: 0.7334 (mtm) REVERT: B 162 CYS cc_start: 0.9245 (m) cc_final: 0.8846 (m) REVERT: B 271 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: B 297 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 50 MET cc_start: 0.8686 (mtt) cc_final: 0.8410 (mtp) REVERT: D 67 MET cc_start: 0.9323 (mmm) cc_final: 0.8791 (mmm) REVERT: D 71 MET cc_start: 0.9030 (mtm) cc_final: 0.8575 (mtm) REVERT: D 142 MET cc_start: 0.8039 (pmm) cc_final: 0.7732 (pmm) REVERT: E 109 MET cc_start: 0.7652 (tpp) cc_final: 0.6803 (mtt) REVERT: E 289 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8808 (mm-30) REVERT: E 297 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7269 (tm-30) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.0991 time to fit residues: 17.6962 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain C residue 239 VAL 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 271 MET Chi-restraints excluded: chain D residue 262 VAL 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 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 101 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048747 restraints weight = 77970.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.050042 restraints weight = 43691.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050923 restraints weight = 29825.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.051493 restraints weight = 23179.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051909 restraints weight = 19612.960| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15089 Z= 0.107 Angle : 0.664 11.797 20461 Z= 0.305 Chirality : 0.048 0.351 2335 Planarity : 0.003 0.029 2510 Dihedral : 10.448 153.788 2377 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.06 % Allowed : 16.68 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1800 helix: 1.85 (0.15), residues: 1155 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 645 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 0.010 0.001 PHE D 111 TRP 0.003 0.001 TRP B 260 HIS 0.008 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (15089) covalent geometry : angle 0.66396 / 0.31 (20461) hydrogen bonds : bond 0.03006 / 2.03 ( 880) hydrogen bonds : angle 3.41961 / 2.37 ( 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 124 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8897 (mtp) cc_final: 0.8527 (mtp) REVERT: C 105 ASN cc_start: 0.6570 (OUTLIER) cc_final: 0.5760 (p0) REVERT: C 142 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: C 271 MET cc_start: 0.9368 (mmm) cc_final: 0.8869 (tpp) REVERT: A 1 MET cc_start: 0.6826 (pmm) cc_final: 0.6010 (ptm) REVERT: A 48 CYS cc_start: 0.8087 (m) cc_final: 0.7766 (t) REVERT: A 109 MET cc_start: 0.6690 (mmt) cc_final: 0.6486 (mmp) REVERT: A 257 MET cc_start: 0.8735 (mmt) cc_final: 0.8430 (mmt) REVERT: B 162 CYS cc_start: 0.9239 (m) cc_final: 0.8876 (m) REVERT: B 271 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7498 (mtp) REVERT: B 297 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 305 ASN cc_start: 0.8581 (m-40) cc_final: 0.7751 (p0) REVERT: D 50 MET cc_start: 0.8637 (mtt) cc_final: 0.8366 (mtp) REVERT: D 67 MET cc_start: 0.9293 (mmm) cc_final: 0.8650 (mmm) REVERT: D 71 MET cc_start: 0.9019 (mtm) cc_final: 0.8588 (mtm) REVERT: D 142 MET cc_start: 0.7719 (pmm) cc_final: 0.7404 (pmm) REVERT: E 109 MET cc_start: 0.7517 (tpp) cc_final: 0.6728 (mtt) REVERT: E 289 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8820 (mm-30) REVERT: E 297 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7162 (tm-30) outliers start: 16 outliers final: 13 residues processed: 120 average time/residue: 0.1032 time to fit residues: 19.0650 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 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: 0.9990 chunk 79 optimal weight: 0.0470 chunk 118 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 140 optimal weight: 0.0970 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.062713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048477 restraints weight = 78167.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049770 restraints weight = 44027.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050637 restraints weight = 30207.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051223 restraints weight = 23603.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051606 restraints weight = 20023.759| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15089 Z= 0.114 Angle : 0.662 11.367 20461 Z= 0.307 Chirality : 0.048 0.367 2335 Planarity : 0.003 0.029 2510 Dihedral : 10.426 154.261 2377 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.13 % Allowed : 17.01 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1800 helix: 1.86 (0.15), residues: 1155 sheet: None (None), residues: 0 loop : -1.95 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.011 0.001 TYR C 288 PHE 0.008 0.001 PHE B 223 TRP 0.004 0.001 TRP D 260 HIS 0.009 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15089) covalent geometry : angle 0.66188 / 0.31 (20461) hydrogen bonds : bond 0.03146 / 2.12 ( 880) hydrogen bonds : angle 3.46449 / 2.40 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.82 seconds wall clock time: 40 minutes 18.17 seconds (2418.17 seconds total)