Starting phenix.real_space_refine on Sat Dec 28 04:20:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eje_31160/12_2024/7eje_31160.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eje_31160/12_2024/7eje_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7eje_31160/12_2024/7eje_31160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eje_31160/12_2024/7eje_31160.map" model { file = "/net/cci-nas-00/data/ceres_data/7eje_31160/12_2024/7eje_31160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eje_31160/12_2024/7eje_31160.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7602 Number of models: 1 Model: "" Number of chains: 6 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: "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} Restraints were copied for chains: B, C Time building chain proxies: 5.54, per 1000 atoms: 0.73 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: 2.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 2.58 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: 2.49 Time building geometry restraints manager: 2.47 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: 10256 3.16 - 6.33: 257 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: 4528 32.88 - 65.76: 174 65.76 - 98.64: 11 98.64 - 131.51: 0 131.51 - 164.39: 3 Dihedral angle restraints: 4716 sinusoidal: 2055 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 4713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1004 0.066 - 0.132: 189 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.000 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 7750 Z= 0.556 Angle : 1.298 15.821 10552 Z= 0.838 Chirality : 0.052 0.331 1203 Planarity : 0.005 0.047 1296 Dihedral : 15.521 164.392 3012 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 41.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.002 HIS A 138 PHE 0.020 0.002 PHE A 259 TYR 0.031 0.004 TYR A 315 ARG 0.007 0.001 ARG A 170 *********************** 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 : 0.936 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 220 ILE cc_start: 0.9123 (mt) cc_final: 0.8756 (mp) REVERT: A 266 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8126 (m) REVERT: A 290 ASN cc_start: 0.7529 (m110) cc_final: 0.7262 (m110) REVERT: B 171 LEU cc_start: 0.8804 (mt) cc_final: 0.8331 (mt) REVERT: B 220 ILE cc_start: 0.8980 (mt) cc_final: 0.8519 (mt) REVERT: B 266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7995 (m) REVERT: C 291 ILE cc_start: 0.9330 (mt) cc_final: 0.8868 (tt) REVERT: C 301 TYR cc_start: 0.8033 (t80) cc_final: 0.7759 (t80) outliers start: 33 outliers final: 8 residues processed: 310 average time/residue: 0.2923 time to fit residues: 111.3980 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 : 0.891 ------------------------------------------------------------------------------- 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 78 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS 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 200 GLN C 267 ASN C 313 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7750 Z= 0.304 Angle : 0.785 7.783 10552 Z= 0.417 Chirality : 0.043 0.153 1203 Planarity : 0.006 0.055 1296 Dihedral : 17.966 179.491 1345 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.37 % Favored : 95.66 % Rotamer: Outliers : 3.49 % Allowed : 13.84 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.25), residues: 921 helix: -0.52 (0.22), residues: 426 sheet: -0.94 (0.44), residues: 126 loop : -0.57 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 294 PHE 0.025 0.003 PHE A 126 TYR 0.021 0.002 TYR C 315 ARG 0.008 0.001 ARG A 130 *********************** 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 196 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.909 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 129 PHE cc_start: 0.8114 (p90) cc_final: 0.7752 (p90) REVERT: A 218 LEU cc_start: 0.8648 (tp) cc_final: 0.8413 (tp) REVERT: B 124 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7459 (mm-30) REVERT: B 171 LEU cc_start: 0.8863 (mt) cc_final: 0.8389 (mt) REVERT: B 189 VAL cc_start: 0.8556 (t) cc_final: 0.8321 (t) REVERT: B 315 TYR cc_start: 0.6807 (m-10) cc_final: 0.6574 (m-10) outliers start: 26 outliers final: 12 residues processed: 185 average time/residue: 0.2068 time to fit residues: 51.1869 Evaluate side-chains 144 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 0.0010 chunk 23 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7750 Z= 0.192 Angle : 0.676 7.280 10552 Z= 0.353 Chirality : 0.040 0.148 1203 Planarity : 0.004 0.053 1296 Dihedral : 17.231 179.514 1323 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.91 % Favored : 95.11 % Rotamer: Outliers : 4.03 % Allowed : 15.99 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 921 helix: 0.40 (0.25), residues: 408 sheet: -0.61 (0.44), residues: 129 loop : -0.73 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 47 PHE 0.014 0.002 PHE C 92 TYR 0.020 0.002 TYR A 191 ARG 0.005 0.001 ARG A 130 *********************** 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 192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.908 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 159 TYR cc_start: 0.8266 (t80) cc_final: 0.7881 (t80) REVERT: A 189 VAL cc_start: 0.8198 (t) cc_final: 0.7979 (t) REVERT: A 228 TYR cc_start: 0.8460 (m-80) cc_final: 0.8138 (m-80) REVERT: A 314 ILE cc_start: 0.8515 (mt) cc_final: 0.8204 (tt) REVERT: B 189 VAL cc_start: 0.8497 (t) cc_final: 0.8295 (t) REVERT: C 159 TYR cc_start: 0.7879 (t80) cc_final: 0.7561 (t80) outliers start: 30 outliers final: 16 residues processed: 178 average time/residue: 0.1989 time to fit residues: 47.5662 Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN 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 104 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 0.0770 chunk 40 optimal weight: 8.9990 chunk 56 optimal weight: 0.0020 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 1.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7750 Z= 0.212 Angle : 0.653 7.421 10552 Z= 0.338 Chirality : 0.040 0.160 1203 Planarity : 0.004 0.053 1296 Dihedral : 17.012 174.694 1323 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.47 % Favored : 95.55 % Rotamer: Outliers : 3.90 % Allowed : 17.20 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 921 helix: 0.64 (0.25), residues: 420 sheet: -0.58 (0.47), residues: 114 loop : -0.69 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 47 PHE 0.010 0.002 PHE A 195 TYR 0.026 0.002 TYR B 54 ARG 0.007 0.001 ARG B 299 *********************** 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 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 TYR cc_start: 0.7769 (t80) cc_final: 0.7531 (t80) REVERT: C 235 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6380 (ptt-90) REVERT: C 301 TYR cc_start: 0.8155 (t80) cc_final: 0.7927 (t80) outliers start: 29 outliers final: 18 residues processed: 162 average time/residue: 0.2063 time to fit residues: 44.8408 Evaluate side-chains 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN 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 315 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 257 ASP 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 102 ILE Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 235 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN A 196 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7750 Z= 0.185 Angle : 0.650 7.745 10552 Z= 0.333 Chirality : 0.039 0.152 1203 Planarity : 0.004 0.054 1296 Dihedral : 16.636 173.246 1323 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.02 % Favored : 95.01 % Rotamer: Outliers : 4.03 % Allowed : 18.28 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 921 helix: 0.81 (0.26), residues: 405 sheet: -0.41 (0.47), residues: 117 loop : -0.79 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.010 0.002 PHE A 195 TYR 0.024 0.002 TYR B 54 ARG 0.005 0.001 ARG A 130 *********************** 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 179 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.8757 (mt) cc_final: 0.8351 (mt) REVERT: C 159 TYR cc_start: 0.7704 (t80) cc_final: 0.7451 (t80) REVERT: C 235 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.5956 (ptt-90) outliers start: 30 outliers final: 19 residues processed: 168 average time/residue: 0.2233 time to fit residues: 50.3543 Evaluate side-chains 147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN 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 220 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 291 ILE 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 195 PHE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 235 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7750 Z= 0.361 Angle : 0.739 7.661 10552 Z= 0.378 Chirality : 0.042 0.163 1203 Planarity : 0.005 0.053 1296 Dihedral : 16.826 170.953 1323 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.32 % Favored : 93.70 % Rotamer: Outliers : 5.38 % Allowed : 18.41 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 921 helix: 0.79 (0.25), residues: 414 sheet: -0.58 (0.48), residues: 117 loop : -0.89 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.014 0.002 PHE A 195 TYR 0.025 0.002 TYR B 54 ARG 0.005 0.001 ARG A 130 *********************** 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 161 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 31 residues processed: 145 average time/residue: 0.2047 time to fit residues: 40.6133 Evaluate side-chains 148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR 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 64 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7750 Z= 0.238 Angle : 0.678 8.090 10552 Z= 0.348 Chirality : 0.040 0.156 1203 Planarity : 0.004 0.055 1296 Dihedral : 16.544 168.775 1323 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.34 % Favored : 94.68 % Rotamer: Outliers : 4.44 % Allowed : 19.62 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 921 helix: 0.81 (0.25), residues: 414 sheet: -0.31 (0.50), residues: 114 loop : -0.86 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.016 0.002 PHE A 195 TYR 0.026 0.002 TYR B 54 ARG 0.002 0.000 ARG B 170 *********************** 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 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7193 (mtp) cc_final: 0.6848 (mtp) REVERT: C 159 TYR cc_start: 0.8102 (t80) cc_final: 0.7851 (t80) outliers start: 33 outliers final: 27 residues processed: 136 average time/residue: 0.2013 time to fit residues: 38.0438 Evaluate side-chains 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 72 ASP 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 220 ILE Chi-restraints excluded: chain A residue 238 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 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN 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 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7750 Z= 0.186 Angle : 0.667 9.552 10552 Z= 0.341 Chirality : 0.040 0.151 1203 Planarity : 0.004 0.057 1296 Dihedral : 16.204 171.924 1323 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.13 % Favored : 94.90 % Rotamer: Outliers : 4.30 % Allowed : 20.43 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 921 helix: 0.86 (0.25), residues: 414 sheet: -0.08 (0.46), residues: 126 loop : -0.75 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.018 0.002 PHE A 195 TYR 0.027 0.002 TYR B 54 ARG 0.003 0.000 ARG C 235 *********************** 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 166 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7122 (mtp) cc_final: 0.6764 (mtp) outliers start: 32 outliers final: 25 residues processed: 153 average time/residue: 0.2202 time to fit residues: 45.0261 Evaluate side-chains 145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 238 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 64 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 196 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7750 Z= 0.193 Angle : 0.677 8.459 10552 Z= 0.347 Chirality : 0.040 0.152 1203 Planarity : 0.004 0.057 1296 Dihedral : 16.097 172.387 1323 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.13 % Favored : 94.90 % Rotamer: Outliers : 4.30 % Allowed : 20.70 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 921 helix: 1.16 (0.26), residues: 396 sheet: -0.47 (0.40), residues: 162 loop : -0.50 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 47 PHE 0.008 0.001 PHE A 195 TYR 0.028 0.002 TYR B 54 ARG 0.005 0.000 ARG B 299 *********************** 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 163 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8518 (m-80) cc_final: 0.8166 (m-80) REVERT: B 238 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8599 (tp) outliers start: 32 outliers final: 26 residues processed: 149 average time/residue: 0.1945 time to fit residues: 39.8630 Evaluate side-chains 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN 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 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.7692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7750 Z= 0.253 Angle : 0.706 10.589 10552 Z= 0.362 Chirality : 0.040 0.153 1203 Planarity : 0.004 0.055 1296 Dihedral : 15.899 163.083 1323 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.89 % Favored : 94.14 % Rotamer: Outliers : 3.76 % Allowed : 21.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.27), residues: 921 helix: 1.07 (0.25), residues: 414 sheet: -0.40 (0.40), residues: 162 loop : -0.46 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.035 0.002 PHE C 259 TYR 0.029 0.002 TYR B 54 ARG 0.012 0.000 ARG C 299 ********************** 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 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8836 (tp) outliers start: 28 outliers final: 26 residues processed: 140 average time/residue: 0.1885 time to fit residues: 36.4346 Evaluate side-chains 151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN 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 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 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 = 0.3310 r_free = 0.3310 target = 0.081887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065576 restraints weight = 21380.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.067823 restraints weight = 11749.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069415 restraints weight = 7896.001| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7750 Z= 0.243 Angle : 0.700 10.883 10552 Z= 0.359 Chirality : 0.040 0.137 1203 Planarity : 0.004 0.053 1296 Dihedral : 15.914 167.665 1323 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.45 % Favored : 94.57 % Rotamer: Outliers : 3.76 % Allowed : 21.77 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 921 helix: 1.06 (0.25), residues: 417 sheet: -0.31 (0.40), residues: 162 loop : -0.38 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.031 0.002 PHE A 259 TYR 0.029 0.002 TYR B 54 ARG 0.012 0.000 ARG C 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.67 seconds wall clock time: 34 minutes 59.30 seconds (2099.30 seconds total)