Starting phenix.real_space_refine on Fri Sep 11 04:43:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.cif" model { file = "/net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eje_31160/09_2026/7eje_31160.map" } resolution = 3.98 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4677 2.51 5 N 1341 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.67, per 1000 atoms: 0.22 Number of scatterers: 7602 At special positions: 0 Unit cell: (107.092, 75.748, 114.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 27 15.00 Mg 3 11.99 O 1515 8.00 N 1341 7.00 C 4677 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 292.1 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 52.2% alpha, 11.8% beta 8 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.776A pdb=" N ILE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.561A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.855A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.573A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.535A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.962A pdb=" N ARG A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.923A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 34 through 42 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.776A pdb=" N ILE B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.562A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.854A pdb=" N ASN B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.573A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.535A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.961A pdb=" N ARG B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.922A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.775A pdb=" N ILE C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.563A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 removed outlier: 3.854A pdb=" N ASN C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.573A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.536A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.960A pdb=" N ARG C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.924A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126 removed outlier: 8.366A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 126 removed outlier: 8.367A pdb=" N VAL B 264 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA B 157 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA B 192 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR B 159 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 299 through 304 Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126 removed outlier: 8.367A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 299 through 304 Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 330 311 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2393 1.33 - 1.45: 1187 1.45 - 1.57: 4055 1.57 - 1.69: 52 1.69 - 1.81: 63 Bond restraints: 7750 Sorted by residual: bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O3A ANP C 403 " pdb=" PB ANP C 403 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C MET B 158 " pdb=" N TYR B 159 " ideal model delta sigma weight residual 1.332 1.253 0.079 1.31e-02 5.83e+03 3.63e+01 bond pdb=" C MET C 158 " pdb=" N TYR C 159 " ideal model delta sigma weight residual 1.332 1.254 0.078 1.31e-02 5.83e+03 3.51e+01 ... (remaining 7745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 10255 3.16 - 6.33: 258 6.33 - 9.49: 30 9.49 - 12.66: 6 12.66 - 15.82: 3 Bond angle restraints: 10552 Sorted by residual: angle pdb=" C LYS B 285 " pdb=" N PRO B 286 " pdb=" CA PRO B 286 " ideal model delta sigma weight residual 119.78 126.62 -6.84 1.03e+00 9.43e-01 4.41e+01 angle pdb=" C LYS A 285 " pdb=" N PRO A 286 " pdb=" CA PRO A 286 " ideal model delta sigma weight residual 119.78 126.62 -6.84 1.03e+00 9.43e-01 4.41e+01 angle pdb=" C LYS C 285 " pdb=" N PRO C 286 " pdb=" CA PRO C 286 " ideal model delta sigma weight residual 119.78 126.59 -6.81 1.03e+00 9.43e-01 4.37e+01 angle pdb=" N GLU C 124 " pdb=" CA GLU C 124 " pdb=" C GLU C 124 " ideal model delta sigma weight residual 108.48 118.33 -9.85 1.80e+00 3.09e-01 2.99e+01 angle pdb=" N GLU B 124 " pdb=" CA GLU B 124 " pdb=" C GLU B 124 " ideal model delta sigma weight residual 108.48 118.33 -9.85 1.80e+00 3.09e-01 2.99e+01 ... (remaining 10547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.88: 4456 32.88 - 65.76: 162 65.76 - 98.64: 11 98.64 - 131.51: 0 131.51 - 164.39: 3 Dihedral angle restraints: 4632 sinusoidal: 1971 harmonic: 2661 Sorted by residual: dihedral pdb=" CA ILE B 314 " pdb=" C ILE B 314 " pdb=" N TYR B 315 " pdb=" CA TYR B 315 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ILE A 314 " pdb=" C ILE A 314 " pdb=" N TYR A 315 " pdb=" CA TYR A 315 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE C 314 " pdb=" C ILE C 314 " pdb=" N TYR C 315 " pdb=" CA TYR C 315 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 999 0.066 - 0.132: 194 0.132 - 0.198: 4 0.198 - 0.265: 3 0.265 - 0.331: 3 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' ANP C 403 " pdb=" C2' ANP C 403 " pdb=" C4' ANP C 403 " pdb=" O3' ANP C 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1200 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 158 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C MET B 158 " -0.052 2.00e-02 2.50e+03 pdb=" O MET B 158 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR B 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 158 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C MET A 158 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 158 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 158 " 0.014 2.00e-02 2.50e+03 2.96e-02 8.79e+00 pdb=" C MET C 158 " -0.051 2.00e-02 2.50e+03 pdb=" O MET C 158 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR C 159 " 0.018 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 69 2.14 - 2.83: 2638 2.83 - 3.52: 10853 3.52 - 4.21: 17854 4.21 - 4.90: 30158 Nonbonded interactions: 61572 Sorted by model distance: nonbonded pdb=" O ALA B 217 " pdb=" CG1 VAL B 261 " model vdw 1.454 3.460 nonbonded pdb=" O ALA C 217 " pdb=" CG1 VAL C 261 " model vdw 1.454 3.460 nonbonded pdb=" O ALA A 217 " pdb=" CG1 VAL A 261 " model vdw 1.454 3.460 nonbonded pdb=" CG2 VAL C 270 " pdb=" CG2 ILE C 287 " model vdw 1.579 3.880 nonbonded pdb=" CG2 VAL A 270 " pdb=" CG2 ILE A 287 " model vdw 1.579 3.880 ... (remaining 61567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = (chain 'C' and resid 22 through 336) } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.009 0.148 7752 Z= 0.590 Angle : 1.302 15.821 10552 Z= 0.856 Chirality : 0.053 0.331 1203 Planarity : 0.005 0.047 1296 Dihedral : 15.343 164.392 2928 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 42.12 Ramachandran Plot: Outliers : 2.28 % Allowed : 4.89 % Favored : 92.83 % Rotamer: Outliers : 4.44 % Allowed : 2.82 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -2.37 (0.25), residues: 921 helix: -2.32 (0.16), residues: 408 sheet: -2.56 (0.47), residues: 114 loop : -0.07 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 170 TYR 0.031 0.004 TYR A 315 PHE 0.020 0.002 PHE A 259 HIS 0.005 0.002 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00901 / 0.57 ( 7750) covalent geometry : angle 1.30153 / 0.86 (10552) hydrogen bonds : bond 0.15732 / 10.70 ( 327) hydrogen bonds : angle 9.94827 / 7.21 ( 887) Misc. bond : bond 0.09494 / 6.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.259 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: A 220 ILE cc_start: 0.9122 (mt) cc_final: 0.8762 (mp) REVERT: A 266 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 171 LEU cc_start: 0.8804 (mt) cc_final: 0.8332 (mt) REVERT: B 220 ILE cc_start: 0.8979 (mt) cc_final: 0.8526 (mt) REVERT: B 266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7992 (m) REVERT: C 291 ILE cc_start: 0.9330 (mt) cc_final: 0.8870 (tt) REVERT: C 301 TYR cc_start: 0.8033 (t80) cc_final: 0.7760 (t80) outliers start: 33 outliers final: 8 residues processed: 310 average time/residue: 0.1138 time to fit residues: 43.7253 Evaluate side-chains 164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 263 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 HIS ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 313 GLN B 36 ASN B 93 HIS B 200 GLN B 267 ASN B 313 GLN C 47 HIS C 93 HIS C 200 GLN C 267 ASN C 313 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.068691 restraints weight = 21774.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071132 restraints weight = 11406.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072790 restraints weight = 7352.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073875 restraints weight = 5435.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074659 restraints weight = 4425.098| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7752 Z= 0.212 Angle : 0.893 9.241 10552 Z= 0.468 Chirality : 0.048 0.174 1203 Planarity : 0.007 0.086 1296 Dihedral : 17.641 176.772 1261 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 1.19 % Allowed : 3.80 % Favored : 95.01 % Rotamer: Outliers : 4.30 % Allowed : 11.83 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.26), residues: 921 helix: -0.87 (0.22), residues: 405 sheet: -0.89 (0.44), residues: 126 loop : -0.68 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 130 TYR 0.030 0.003 TYR A 216 PHE 0.032 0.003 PHE B 126 HIS 0.010 0.002 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 ( 7750) covalent geometry : angle 0.89275 / 0.47 (10552) hydrogen bonds : bond 0.04513 / 2.95 ( 327) hydrogen bonds : angle 6.48679 / 4.76 ( 887) Misc. bond : bond 0.00682 / 0.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.208 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: A 39 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9140 (pttp) REVERT: A 59 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 124 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8333 (mm-30) REVERT: A 158 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7888 (mtp) REVERT: A 191 TYR cc_start: 0.8998 (t80) cc_final: 0.8773 (t80) REVERT: A 218 LEU cc_start: 0.9505 (tp) cc_final: 0.9025 (tp) REVERT: A 228 TYR cc_start: 0.8772 (m-80) cc_final: 0.8376 (m-80) REVERT: A 290 ASN cc_start: 0.8719 (m-40) cc_final: 0.8438 (m110) REVERT: A 301 TYR cc_start: 0.8667 (t80) cc_final: 0.8372 (t80) REVERT: A 326 MET cc_start: 0.8287 (mmm) cc_final: 0.8081 (mmm) REVERT: B 124 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 158 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7876 (ptp) REVERT: B 171 LEU cc_start: 0.9618 (mt) cc_final: 0.9397 (mt) REVERT: B 191 TYR cc_start: 0.8811 (t80) cc_final: 0.8367 (t80) REVERT: B 220 ILE cc_start: 0.9571 (mt) cc_final: 0.9212 (mm) REVERT: B 235 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8015 (pmt-80) REVERT: B 301 TYR cc_start: 0.8685 (t80) cc_final: 0.8327 (t80) REVERT: C 220 ILE cc_start: 0.9567 (mt) cc_final: 0.9285 (mm) REVERT: C 235 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7292 (pmt170) outliers start: 32 outliers final: 15 residues processed: 193 average time/residue: 0.0796 time to fit residues: 20.8819 Evaluate side-chains 164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 330 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.068084 restraints weight = 21317.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070525 restraints weight = 11360.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072149 restraints weight = 7411.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.073227 restraints weight = 5518.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074047 restraints weight = 4519.259| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7752 Z= 0.163 Angle : 0.757 7.971 10552 Z= 0.396 Chirality : 0.043 0.150 1203 Planarity : 0.005 0.065 1296 Dihedral : 17.479 179.801 1253 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.45 % Favored : 94.57 % Rotamer: Outliers : 4.03 % Allowed : 16.13 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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 (0.26), residues: 921 helix: -0.35 (0.23), residues: 423 sheet: -0.22 (0.46), residues: 126 loop : -0.76 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.023 0.003 TYR B 54 PHE 0.017 0.002 PHE C 126 HIS 0.009 0.002 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7750) covalent geometry : angle 0.75713 / 0.40 (10552) hydrogen bonds : bond 0.03848 / 2.56 ( 327) hydrogen bonds : angle 5.75138 / 4.26 ( 887) Misc. bond : bond 0.00329 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.231 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: A 39 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8978 (pttm) REVERT: A 59 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 137 CYS cc_start: 0.9180 (m) cc_final: 0.8687 (t) REVERT: A 158 MET cc_start: 0.8251 (ptt) cc_final: 0.7939 (ptm) REVERT: A 159 TYR cc_start: 0.9150 (t80) cc_final: 0.8207 (t80) REVERT: A 191 TYR cc_start: 0.8940 (t80) cc_final: 0.8725 (t80) REVERT: A 228 TYR cc_start: 0.8802 (m-80) cc_final: 0.8540 (m-80) REVERT: A 326 MET cc_start: 0.8273 (mmm) cc_final: 0.8062 (mmm) REVERT: B 124 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8122 (tt0) REVERT: B 171 LEU cc_start: 0.9574 (mt) cc_final: 0.9341 (mt) REVERT: B 235 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7893 (ptt-90) REVERT: B 301 TYR cc_start: 0.8692 (t80) cc_final: 0.8398 (t80) REVERT: C 301 TYR cc_start: 0.8863 (t80) cc_final: 0.8561 (t80) outliers start: 30 outliers final: 11 residues processed: 174 average time/residue: 0.0841 time to fit residues: 19.7307 Evaluate side-chains 151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065546 restraints weight = 21939.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.067922 restraints weight = 11822.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.069508 restraints weight = 7806.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.070495 restraints weight = 5886.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071245 restraints weight = 4894.485| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7752 Z= 0.199 Angle : 0.723 6.960 10552 Z= 0.378 Chirality : 0.043 0.157 1203 Planarity : 0.005 0.053 1296 Dihedral : 17.304 179.578 1243 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer: Outliers : 4.70 % Allowed : 16.13 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -0.53 (0.27), residues: 921 helix: 0.17 (0.25), residues: 423 sheet: -0.29 (0.46), residues: 126 loop : -0.84 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.035 0.002 TYR C 54 PHE 0.024 0.002 PHE C 259 HIS 0.004 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 7750) covalent geometry : angle 0.72331 / 0.38 (10552) hydrogen bonds : bond 0.03692 / 2.44 ( 327) hydrogen bonds : angle 5.24804 / 3.89 ( 887) Misc. bond : bond 0.00590 / 0.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.238 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: A 39 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9021 (pttm) REVERT: A 59 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 124 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8407 (mm-30) REVERT: A 137 CYS cc_start: 0.9231 (m) cc_final: 0.8763 (t) REVERT: A 158 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7911 (ptm) REVERT: A 159 TYR cc_start: 0.9158 (t80) cc_final: 0.8364 (t80) REVERT: A 210 MET cc_start: 0.7895 (mtp) cc_final: 0.7557 (ttm) REVERT: A 228 TYR cc_start: 0.8997 (m-80) cc_final: 0.8666 (m-80) REVERT: A 326 MET cc_start: 0.8265 (mmm) cc_final: 0.8036 (mmm) REVERT: B 54 TYR cc_start: 0.8641 (m-80) cc_final: 0.8389 (m-80) REVERT: B 124 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: B 158 MET cc_start: 0.8241 (ptp) cc_final: 0.8018 (ptp) REVERT: B 171 LEU cc_start: 0.9592 (mt) cc_final: 0.9368 (mt) REVERT: B 251 MET cc_start: 0.8654 (mtt) cc_final: 0.8429 (mmm) REVERT: C 301 TYR cc_start: 0.8912 (t80) cc_final: 0.8681 (t80) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 0.0808 time to fit residues: 17.3708 Evaluate side-chains 148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066741 restraints weight = 21428.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.069142 restraints weight = 11680.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.070703 restraints weight = 7709.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.071705 restraints weight = 5802.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.072563 restraints weight = 4802.435| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7752 Z= 0.135 Angle : 0.692 7.249 10552 Z= 0.359 Chirality : 0.042 0.207 1203 Planarity : 0.004 0.050 1296 Dihedral : 17.163 179.660 1239 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.13 % Favored : 94.90 % Rotamer: Outliers : 5.24 % Allowed : 16.94 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -0.42 (0.27), residues: 921 helix: 0.30 (0.25), residues: 423 sheet: -0.42 (0.49), residues: 117 loop : -0.77 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 130 TYR 0.042 0.002 TYR C 54 PHE 0.015 0.002 PHE C 259 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 7750) covalent geometry : angle 0.69176 / 0.36 (10552) hydrogen bonds : bond 0.03392 / 2.24 ( 327) hydrogen bonds : angle 5.10457 / 3.78 ( 887) Misc. bond : bond 0.00373 / 0.26 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.184 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: A 39 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9034 (pttm) REVERT: A 59 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 137 CYS cc_start: 0.9232 (m) cc_final: 0.8745 (t) REVERT: A 159 TYR cc_start: 0.9143 (t80) cc_final: 0.8323 (t80) REVERT: A 228 TYR cc_start: 0.8893 (m-80) cc_final: 0.8620 (m-80) REVERT: A 304 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7766 (ttmm) REVERT: A 314 ILE cc_start: 0.9384 (mt) cc_final: 0.8952 (tt) REVERT: B 124 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 158 MET cc_start: 0.8256 (ptp) cc_final: 0.8004 (ptp) REVERT: C 253 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9264 (mm) REVERT: C 301 TYR cc_start: 0.8861 (t80) cc_final: 0.8652 (t80) outliers start: 39 outliers final: 25 residues processed: 161 average time/residue: 0.0787 time to fit residues: 17.6132 Evaluate side-chains 161 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066699 restraints weight = 21325.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069082 restraints weight = 11604.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070667 restraints weight = 7664.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071720 restraints weight = 5752.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.072535 restraints weight = 4717.534| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7752 Z= 0.132 Angle : 0.690 10.445 10552 Z= 0.354 Chirality : 0.041 0.170 1203 Planarity : 0.004 0.051 1296 Dihedral : 17.060 179.658 1239 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.91 % Favored : 95.11 % Rotamer: Outliers : 5.24 % Allowed : 18.15 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -0.15 (0.27), residues: 921 helix: 0.69 (0.26), residues: 405 sheet: -0.30 (0.49), residues: 117 loop : -0.78 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.027 0.002 TYR B 191 PHE 0.014 0.002 PHE B 195 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7750) covalent geometry : angle 0.68951 / 0.35 (10552) hydrogen bonds : bond 0.03041 / 1.99 ( 327) hydrogen bonds : angle 4.92303 / 3.68 ( 887) Misc. bond : bond 0.00361 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9045 (pttm) REVERT: A 59 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 137 CYS cc_start: 0.9241 (m) cc_final: 0.8769 (t) REVERT: A 158 MET cc_start: 0.8008 (ptp) cc_final: 0.7558 (mtp) REVERT: A 159 TYR cc_start: 0.9126 (t80) cc_final: 0.8268 (t80) REVERT: A 219 LEU cc_start: 0.9485 (tp) cc_final: 0.9231 (tt) REVERT: A 228 TYR cc_start: 0.8886 (m-80) cc_final: 0.8657 (m-80) REVERT: A 304 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7692 (ttmm) REVERT: A 314 ILE cc_start: 0.9385 (mt) cc_final: 0.8944 (tt) REVERT: B 124 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: B 142 VAL cc_start: 0.9404 (t) cc_final: 0.9182 (p) REVERT: B 204 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9408 (mm) REVERT: B 251 MET cc_start: 0.8636 (mtt) cc_final: 0.8430 (mmm) REVERT: C 124 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8000 (tt0) REVERT: C 171 LEU cc_start: 0.9344 (mp) cc_final: 0.8789 (mt) REVERT: C 253 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9290 (mm) outliers start: 39 outliers final: 26 residues processed: 157 average time/residue: 0.0750 time to fit residues: 16.4068 Evaluate side-chains 162 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.064006 restraints weight = 21823.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.066305 restraints weight = 11857.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067862 restraints weight = 7827.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068789 restraints weight = 5862.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.069581 restraints weight = 4871.009| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7752 Z= 0.238 Angle : 0.766 12.649 10552 Z= 0.389 Chirality : 0.043 0.167 1203 Planarity : 0.005 0.051 1296 Dihedral : 17.014 179.458 1239 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.78 % Favored : 94.25 % Rotamer: Outliers : 5.65 % Allowed : 19.49 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -0.11 (0.27), residues: 921 helix: 0.87 (0.26), residues: 408 sheet: -0.47 (0.48), residues: 117 loop : -0.89 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 130 TYR 0.024 0.002 TYR C 54 PHE 0.017 0.002 PHE A 259 HIS 0.004 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 ( 7750) covalent geometry : angle 0.76616 / 0.39 (10552) hydrogen bonds : bond 0.03526 / 2.32 ( 327) hydrogen bonds : angle 4.99679 / 3.73 ( 887) Misc. bond : bond 0.00386 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9070 (pttm) REVERT: A 59 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 124 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 137 CYS cc_start: 0.9292 (m) cc_final: 0.8769 (t) REVERT: A 158 MET cc_start: 0.8461 (ptp) cc_final: 0.8140 (ptp) REVERT: A 228 TYR cc_start: 0.9135 (m-80) cc_final: 0.8709 (m-80) REVERT: A 304 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7932 (tptp) REVERT: A 326 MET cc_start: 0.8193 (mmm) cc_final: 0.7904 (mmm) REVERT: B 124 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: B 204 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9356 (mm) REVERT: B 218 LEU cc_start: 0.9396 (tp) cc_final: 0.9176 (tp) REVERT: C 253 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9298 (mm) REVERT: C 257 ASP cc_start: 0.8126 (t0) cc_final: 0.7829 (m-30) outliers start: 42 outliers final: 30 residues processed: 143 average time/residue: 0.0764 time to fit residues: 15.3567 Evaluate side-chains 155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065711 restraints weight = 21495.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.068151 restraints weight = 11584.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069790 restraints weight = 7599.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070873 restraints weight = 5666.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071558 restraints weight = 4648.812| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7752 Z= 0.138 Angle : 0.714 11.430 10552 Z= 0.366 Chirality : 0.042 0.171 1203 Planarity : 0.004 0.050 1296 Dihedral : 16.951 178.633 1239 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.45 % Favored : 94.57 % Rotamer: Outliers : 4.84 % Allowed : 20.83 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -0.02 (0.27), residues: 921 helix: 0.90 (0.26), residues: 408 sheet: -0.15 (0.49), residues: 114 loop : -0.87 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.017 0.001 TYR B 54 PHE 0.015 0.002 PHE A 195 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7750) covalent geometry : angle 0.71408 / 0.37 (10552) hydrogen bonds : bond 0.03133 / 2.04 ( 327) hydrogen bonds : angle 4.84945 / 3.62 ( 887) Misc. bond : bond 0.00371 / 0.26 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9064 (pttm) REVERT: A 59 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 124 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8651 (mm-30) REVERT: A 137 CYS cc_start: 0.9337 (m) cc_final: 0.8756 (t) REVERT: A 228 TYR cc_start: 0.9005 (m-80) cc_final: 0.8590 (m-80) REVERT: A 304 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7931 (tptm) REVERT: B 39 LYS cc_start: 0.9462 (ttpp) cc_final: 0.9215 (ptpp) REVERT: B 124 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: B 204 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9320 (mm) REVERT: B 218 LEU cc_start: 0.9371 (tp) cc_final: 0.9132 (tp) REVERT: C 124 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: C 229 ARG cc_start: 0.8461 (mtt180) cc_final: 0.7794 (tpt170) REVERT: C 253 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9279 (mm) outliers start: 36 outliers final: 24 residues processed: 152 average time/residue: 0.0773 time to fit residues: 16.4048 Evaluate side-chains 158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS A 267 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.061693 restraints weight = 22109.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063924 restraints weight = 12142.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065418 restraints weight = 8141.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.066416 restraints weight = 6197.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067070 restraints weight = 5142.480| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 7752 Z= 0.301 Angle : 0.825 10.114 10552 Z= 0.419 Chirality : 0.044 0.190 1203 Planarity : 0.005 0.048 1296 Dihedral : 16.928 176.602 1239 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.65 % Favored : 93.38 % Rotamer: Outliers : 5.11 % Allowed : 20.56 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -0.11 (0.27), residues: 921 helix: 0.97 (0.26), residues: 402 sheet: -0.37 (0.49), residues: 114 loop : -1.01 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 130 TYR 0.032 0.002 TYR B 54 PHE 0.020 0.003 PHE A 195 HIS 0.006 0.002 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 ( 7750) covalent geometry : angle 0.82478 / 0.42 (10552) hydrogen bonds : bond 0.03764 / 2.48 ( 327) hydrogen bonds : angle 5.18144 / 3.84 ( 887) Misc. bond : bond 0.00390 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9079 (pttm) REVERT: A 59 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 137 CYS cc_start: 0.9235 (m) cc_final: 0.8877 (t) REVERT: A 304 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8041 (tptm) REVERT: B 124 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: B 204 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9418 (mm) REVERT: B 218 LEU cc_start: 0.9446 (tp) cc_final: 0.9205 (tp) REVERT: C 253 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9284 (mm) outliers start: 38 outliers final: 26 residues processed: 135 average time/residue: 0.0786 time to fit residues: 14.8482 Evaluate side-chains 144 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 43 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.063773 restraints weight = 21845.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066125 restraints weight = 11869.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.067697 restraints weight = 7876.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068666 restraints weight = 5948.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069488 restraints weight = 4939.440| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7752 Z= 0.159 Angle : 0.758 11.397 10552 Z= 0.385 Chirality : 0.042 0.177 1203 Planarity : 0.004 0.047 1296 Dihedral : 16.895 175.321 1239 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer: Outliers : 4.44 % Allowed : 21.37 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: 0.03 (0.27), residues: 921 helix: 1.03 (0.26), residues: 402 sheet: -0.02 (0.50), residues: 111 loop : -0.95 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.025 0.001 TYR B 54 PHE 0.023 0.002 PHE B 259 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 7750) covalent geometry : angle 0.75795 / 0.38 (10552) hydrogen bonds : bond 0.03279 / 2.15 ( 327) hydrogen bonds : angle 4.89546 / 3.64 ( 887) Misc. bond : bond 0.00377 / 0.26 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9080 (pttm) REVERT: A 124 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8703 (mm-30) REVERT: A 137 CYS cc_start: 0.9323 (m) cc_final: 0.8810 (t) REVERT: A 304 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7935 (tptm) REVERT: B 124 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: B 204 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9352 (mm) REVERT: B 211 MET cc_start: 0.8082 (ttp) cc_final: 0.7681 (ttp) REVERT: B 218 LEU cc_start: 0.9386 (tp) cc_final: 0.9153 (tp) REVERT: C 124 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8003 (tt0) outliers start: 33 outliers final: 25 residues processed: 146 average time/residue: 0.0700 time to fit residues: 14.4422 Evaluate side-chains 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.064909 restraints weight = 21951.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067236 restraints weight = 11987.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068686 restraints weight = 7969.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069790 restraints weight = 6077.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.070383 restraints weight = 5010.265| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7752 Z= 0.147 Angle : 0.744 11.327 10552 Z= 0.380 Chirality : 0.041 0.168 1203 Planarity : 0.004 0.049 1296 Dihedral : 16.815 175.174 1239 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer: Outliers : 4.30 % Allowed : 21.64 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: 0.00 (0.27), residues: 921 helix: 0.95 (0.26), residues: 402 sheet: -0.01 (0.50), residues: 114 loop : -0.93 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.034 0.002 TYR B 54 PHE 0.065 0.002 PHE B 259 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7750) covalent geometry : angle 0.74424 / 0.38 (10552) hydrogen bonds : bond 0.03171 / 2.04 ( 327) hydrogen bonds : angle 4.86859 / 3.61 ( 887) Misc. bond : bond 0.00364 / 0.25 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1125.19 seconds wall clock time: 20 minutes 10.84 seconds (1210.84 seconds total)