Starting phenix.real_space_refine on Sat May 2 21:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yuv_39584/05_2026/8yuv_39584_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yuv_39584/05_2026/8yuv_39584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yuv_39584/05_2026/8yuv_39584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yuv_39584/05_2026/8yuv_39584.map" model { file = "/net/cci-nas-00/data/ceres_data/8yuv_39584/05_2026/8yuv_39584_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yuv_39584/05_2026/8yuv_39584_trim.cif" } resolution = 3.0 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= -0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5766 2.51 5 N 1537 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9041 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2344 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'A1LY4': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 9041 At special positions: 0 Unit cell: (105.456, 121.68, 114.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1678 8.00 N 1537 7.00 C 5766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 188 " distance=2.05 Simple disulfide: pdb=" SG CYS R 384 " - pdb=" SG CYS R 388 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 303.3 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 41.1% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.045A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.731A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.630A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.088A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.110A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.163A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'R' and resid 33 through 62 Processing helix chain 'R' and resid 67 through 86 Processing helix chain 'R' and resid 86 through 98 Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 102 through 136 removed outlier: 3.825A pdb=" N LEU R 106 " --> pdb=" O PHE R 102 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 148 through 173 removed outlier: 3.625A pdb=" N TYR R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 174 through 179 Processing helix chain 'R' and resid 195 through 207 Processing helix chain 'R' and resid 207 through 235 Processing helix chain 'R' and resid 344 through 384 Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 390 through 416 removed outlier: 3.677A pdb=" N LEU R 401 " --> pdb=" O SER R 397 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) Proline residue: R 409 - end of helix Proline residue: R 413 - end of helix Processing helix chain 'R' and resid 416 through 427 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.248A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 234 removed outlier: 5.742A pdb=" N MET A 240 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.704A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.818A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.572A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.654A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.592A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.244A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.382A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.529A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1542 1.31 - 1.44: 2672 1.44 - 1.57: 4932 1.57 - 1.70: 11 1.70 - 1.82: 85 Bond restraints: 9242 Sorted by residual: bond pdb=" NE ARG G 13 " pdb=" CZ ARG G 13 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.61e+01 bond pdb=" CA PHE B 180 " pdb=" CB PHE B 180 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.43e-02 4.89e+03 1.54e+01 bond pdb=" CB ASP B 118 " pdb=" CG ASP B 118 " ideal model delta sigma weight residual 1.516 1.421 0.095 2.50e-02 1.60e+03 1.45e+01 bond pdb=" CA GLN B 175 " pdb=" C GLN B 175 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.18e-02 7.18e+03 1.39e+01 bond pdb=" N THR R 209 " pdb=" CA THR R 209 " ideal model delta sigma weight residual 1.462 1.435 0.027 7.70e-03 1.69e+04 1.25e+01 ... (remaining 9237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 11922 3.05 - 6.09: 560 6.09 - 9.14: 42 9.14 - 12.19: 2 12.19 - 15.23: 1 Bond angle restraints: 12527 Sorted by residual: angle pdb=" N TYR R 194 " pdb=" CA TYR R 194 " pdb=" C TYR R 194 " ideal model delta sigma weight residual 114.39 99.16 15.23 1.45e+00 4.76e-01 1.10e+02 angle pdb=" C ASP G 48 " pdb=" N PRO G 49 " pdb=" CA PRO G 49 " ideal model delta sigma weight residual 119.87 127.96 -8.09 1.04e+00 9.25e-01 6.05e+01 angle pdb=" C SER S 106 " pdb=" N PRO S 107 " pdb=" CA PRO S 107 " ideal model delta sigma weight residual 120.03 126.87 -6.84 9.90e-01 1.02e+00 4.77e+01 angle pdb=" CA PHE R 192 " pdb=" CB PHE R 192 " pdb=" CG PHE R 192 " ideal model delta sigma weight residual 113.80 120.59 -6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" C ASN G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 119.56 125.99 -6.43 1.02e+00 9.61e-01 3.98e+01 ... (remaining 12522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 5379 24.65 - 49.29: 99 49.29 - 73.94: 22 73.94 - 98.58: 6 98.58 - 123.23: 2 Dihedral angle restraints: 5508 sinusoidal: 2185 harmonic: 3323 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 29.02 63.98 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" C02 A1LY4 R 501 " pdb=" C01 A1LY4 R 501 " pdb=" C06 A1LY4 R 501 " pdb=" C05 A1LY4 R 501 " ideal model delta sinusoidal sigma weight residual 52.81 -70.42 123.23 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual 122.80 132.26 -9.46 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 1408 1.000 - 1.999: 0 1.999 - 2.998: 0 2.998 - 3.998: 0 3.998 - 4.997: 1 Chirality restraints: 1409 Sorted by residual: chirality pdb=" C06 A1LY4 R 501 " pdb=" C01 A1LY4 R 501 " pdb=" C05 A1LY4 R 501 " pdb=" C07 A1LY4 R 501 " both_signs ideal model delta sigma weight residual False -2.60 2.40 -5.00 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" CA MET S 192 " pdb=" N MET S 192 " pdb=" C MET S 192 " pdb=" CB MET S 192 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA ILE R 183 " pdb=" N ILE R 183 " pdb=" C ILE R 183 " pdb=" CB ILE R 183 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1406 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.054 2.00e-02 2.50e+03 2.54e-02 1.61e+01 pdb=" CG TRP B 99 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 167 " -0.038 2.00e-02 2.50e+03 2.01e-02 8.11e+00 pdb=" CG TYR R 167 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR R 167 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 167 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR R 167 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR R 167 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR R 167 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 167 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C THR B 196 " 0.045 2.00e-02 2.50e+03 pdb=" O THR B 196 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 197 " -0.016 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2096 2.77 - 3.30: 8386 3.30 - 3.84: 15119 3.84 - 4.37: 18565 4.37 - 4.90: 31510 Nonbonded interactions: 75676 Sorted by model distance: nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.238 3.120 nonbonded pdb=" N TYR R 194 " pdb=" N ASN R 195 " model vdw 2.335 2.560 nonbonded pdb=" OG SER B 201 " pdb=" NE1 TRP B 211 " model vdw 2.435 3.120 nonbonded pdb=" OH TYR R 374 " pdb=" OH TYR R 394 " model vdw 2.436 3.040 nonbonded pdb=" N TYR S 102 " pdb=" O TYR S 102 " model vdw 2.440 2.496 ... (remaining 75671 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.380 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.015 0.103 9246 Z= 0.872 Angle : 1.456 15.233 12535 Z= 0.971 Chirality : 0.162 4.997 1409 Planarity : 0.007 0.057 1577 Dihedral : 11.074 123.230 3354 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.24), residues: 1129 helix: 1.64 (0.23), residues: 416 sheet: 1.89 (0.30), residues: 284 loop : 0.52 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 98 TYR 0.038 0.004 TYR R 167 PHE 0.030 0.004 PHE R 192 TRP 0.054 0.004 TRP B 99 HIS 0.007 0.002 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.01529 ( 9242) covalent geometry : angle 1.45290 (12527) SS BOND : bond 0.03847 ( 4) SS BOND : angle 3.90705 ( 8) hydrogen bonds : bond 0.19073 ( 476) hydrogen bonds : angle 6.32712 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.339 Fit side-chains REVERT: A 17 LYS cc_start: 0.7211 (mttt) cc_final: 0.6966 (mtmm) REVERT: A 22 ASN cc_start: 0.7247 (m-40) cc_final: 0.7021 (m-40) REVERT: A 35 LYS cc_start: 0.8270 (mttp) cc_final: 0.8041 (mptt) REVERT: A 208 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7644 (ttm110) REVERT: A 209 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7437 (mptt) REVERT: A 248 LYS cc_start: 0.7902 (mttt) cc_final: 0.7272 (mptp) REVERT: A 270 LYS cc_start: 0.7880 (mttt) cc_final: 0.7633 (mttm) REVERT: B 154 ASP cc_start: 0.7777 (m-30) cc_final: 0.7575 (m-30) REVERT: B 209 LYS cc_start: 0.8767 (mttm) cc_final: 0.8464 (mtpp) REVERT: S 46 GLU cc_start: 0.7838 (tt0) cc_final: 0.7382 (mt-10) REVERT: S 213 THR cc_start: 0.8521 (m) cc_final: 0.8219 (p) REVERT: R 150 ARG cc_start: 0.7143 (tpp-160) cc_final: 0.6716 (ttp-170) REVERT: R 194 TYR cc_start: 0.5815 (m-80) cc_final: 0.4656 (p90) outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.6019 time to fit residues: 135.3930 Evaluate side-chains 121 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120607 restraints weight = 10071.732| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.30 r_work: 0.2999 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9246 Z= 0.139 Angle : 0.584 7.777 12535 Z= 0.314 Chirality : 0.043 0.148 1409 Planarity : 0.004 0.045 1577 Dihedral : 5.596 59.838 1325 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.05 % Allowed : 12.19 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.25), residues: 1129 helix: 2.53 (0.24), residues: 429 sheet: 1.75 (0.30), residues: 271 loop : 0.43 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.018 0.001 TYR A 290 PHE 0.019 0.002 PHE R 192 TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9242) covalent geometry : angle 0.58263 (12527) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.80960 ( 8) hydrogen bonds : bond 0.05771 ( 476) hydrogen bonds : angle 4.55391 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.315 Fit side-chains REVERT: A 17 LYS cc_start: 0.8225 (mttt) cc_final: 0.7990 (mtmm) REVERT: A 25 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7625 (mp0) REVERT: A 208 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7895 (mtm110) REVERT: A 248 LYS cc_start: 0.8167 (mttt) cc_final: 0.7595 (mptp) REVERT: B 118 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7932 (p0) REVERT: B 217 MET cc_start: 0.7497 (ptt) cc_final: 0.7265 (pmm) REVERT: B 308 LEU cc_start: 0.8702 (mp) cc_final: 0.8315 (mt) REVERT: S 19 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8797 (tttm) REVERT: S 46 GLU cc_start: 0.8546 (tt0) cc_final: 0.8180 (mt-10) REVERT: S 140 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8573 (mtp) REVERT: S 183 GLN cc_start: 0.7862 (mt0) cc_final: 0.7432 (mp10) REVERT: S 213 THR cc_start: 0.8657 (m) cc_final: 0.8324 (p) REVERT: S 215 THR cc_start: 0.8410 (m) cc_final: 0.8011 (p) REVERT: R 153 VAL cc_start: 0.8561 (t) cc_final: 0.8233 (m) outliers start: 20 outliers final: 11 residues processed: 148 average time/residue: 0.5725 time to fit residues: 90.5737 Evaluate side-chains 131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120857 restraints weight = 10019.085| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.56 r_work: 0.2953 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9246 Z= 0.124 Angle : 0.516 6.613 12535 Z= 0.275 Chirality : 0.041 0.152 1409 Planarity : 0.004 0.042 1577 Dihedral : 5.386 59.239 1325 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.07 % Allowed : 13.22 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1129 helix: 2.81 (0.24), residues: 419 sheet: 1.47 (0.30), residues: 278 loop : 0.20 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.013 0.001 TYR S 190 PHE 0.015 0.001 PHE R 192 TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9242) covalent geometry : angle 0.51479 (12527) SS BOND : bond 0.00469 ( 4) SS BOND : angle 1.59726 ( 8) hydrogen bonds : bond 0.04642 ( 476) hydrogen bonds : angle 4.21704 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.413 Fit side-chains REVERT: A 17 LYS cc_start: 0.8048 (mttt) cc_final: 0.7793 (mtmm) REVERT: A 29 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7721 (ttmm) REVERT: A 48 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8396 (t) REVERT: A 208 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7692 (mtm110) REVERT: A 248 LYS cc_start: 0.8060 (mttt) cc_final: 0.7443 (mptp) REVERT: A 273 LEU cc_start: 0.8401 (mp) cc_final: 0.8035 (tp) REVERT: A 298 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7220 (pp20) REVERT: B 118 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7716 (p0) REVERT: B 146 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8866 (tp) REVERT: B 217 MET cc_start: 0.7375 (ptt) cc_final: 0.7082 (pmm) REVERT: B 221 THR cc_start: 0.8745 (m) cc_final: 0.8405 (m) REVERT: B 293 ASN cc_start: 0.7959 (m110) cc_final: 0.7728 (m110) REVERT: S 19 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8680 (tttm) REVERT: S 46 GLU cc_start: 0.8365 (tt0) cc_final: 0.8003 (mt-10) REVERT: S 183 GLN cc_start: 0.7816 (mt0) cc_final: 0.7471 (mp10) REVERT: S 215 THR cc_start: 0.8467 (m) cc_final: 0.8093 (p) REVERT: R 56 MET cc_start: 0.7659 (mtm) cc_final: 0.7387 (mtt) REVERT: R 153 VAL cc_start: 0.8385 (t) cc_final: 0.8147 (m) outliers start: 30 outliers final: 10 residues processed: 137 average time/residue: 0.6154 time to fit residues: 89.9549 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128411 restraints weight = 10063.598| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.23 r_work: 0.2997 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9246 Z= 0.125 Angle : 0.505 6.219 12535 Z= 0.266 Chirality : 0.040 0.145 1409 Planarity : 0.004 0.040 1577 Dihedral : 5.450 59.357 1325 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.18 % Allowed : 14.45 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.25), residues: 1129 helix: 2.83 (0.24), residues: 426 sheet: 1.25 (0.30), residues: 291 loop : 0.23 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.012 0.001 TYR B 264 PHE 0.015 0.001 PHE R 192 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9242) covalent geometry : angle 0.50359 (12527) SS BOND : bond 0.00580 ( 4) SS BOND : angle 1.36410 ( 8) hydrogen bonds : bond 0.04356 ( 476) hydrogen bonds : angle 4.13247 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.349 Fit side-chains REVERT: A 17 LYS cc_start: 0.8128 (mttt) cc_final: 0.7804 (mtmm) REVERT: A 48 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 208 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7659 (ttm110) REVERT: A 248 LYS cc_start: 0.8116 (mttt) cc_final: 0.7527 (mptp) REVERT: A 275 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7372 (mt-10) REVERT: B 75 GLN cc_start: 0.9209 (mm110) cc_final: 0.8980 (tp40) REVERT: B 118 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7705 (p0) REVERT: B 217 MET cc_start: 0.7322 (ptt) cc_final: 0.6824 (pmm) REVERT: B 221 THR cc_start: 0.8808 (m) cc_final: 0.8448 (m) REVERT: B 223 THR cc_start: 0.8318 (t) cc_final: 0.7885 (m) REVERT: B 293 ASN cc_start: 0.8007 (m110) cc_final: 0.7770 (m110) REVERT: G 21 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5845 (tmt) REVERT: S 46 GLU cc_start: 0.8588 (tt0) cc_final: 0.8115 (mt-10) REVERT: S 213 THR cc_start: 0.8642 (m) cc_final: 0.8295 (p) REVERT: S 215 THR cc_start: 0.8366 (m) cc_final: 0.7972 (p) REVERT: R 56 MET cc_start: 0.7728 (mtm) cc_final: 0.7452 (mtt) REVERT: R 90 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8032 (mt) REVERT: R 153 VAL cc_start: 0.8401 (t) cc_final: 0.8155 (m) REVERT: R 194 TYR cc_start: 0.5842 (m-80) cc_final: 0.4412 (p90) outliers start: 31 outliers final: 15 residues processed: 150 average time/residue: 0.5136 time to fit residues: 82.8602 Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 365 SER Chi-restraints excluded: chain R residue 400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 0.0060 chunk 66 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135732 restraints weight = 9901.052| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.05 r_work: 0.3042 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9246 Z= 0.107 Angle : 0.481 6.170 12535 Z= 0.254 Chirality : 0.039 0.140 1409 Planarity : 0.003 0.036 1577 Dihedral : 5.442 59.624 1325 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.97 % Allowed : 15.88 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.25), residues: 1129 helix: 3.00 (0.24), residues: 422 sheet: 1.15 (0.30), residues: 293 loop : 0.07 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.012 0.001 TYR S 190 PHE 0.014 0.001 PHE R 192 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9242) covalent geometry : angle 0.48063 (12527) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.13504 ( 8) hydrogen bonds : bond 0.03981 ( 476) hydrogen bonds : angle 4.05624 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.361 Fit side-chains REVERT: A 17 LYS cc_start: 0.8047 (mttt) cc_final: 0.7716 (mtmm) REVERT: A 48 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 208 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7555 (ttm110) REVERT: A 248 LYS cc_start: 0.8124 (mttt) cc_final: 0.7495 (mptp) REVERT: A 273 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 275 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 318 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8595 (tt0) REVERT: B 75 GLN cc_start: 0.9213 (mm110) cc_final: 0.9004 (tp40) REVERT: B 118 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7677 (p0) REVERT: B 217 MET cc_start: 0.7275 (ptt) cc_final: 0.6777 (pmm) REVERT: B 221 THR cc_start: 0.8785 (m) cc_final: 0.8438 (m) REVERT: B 223 THR cc_start: 0.8215 (t) cc_final: 0.7810 (m) REVERT: B 293 ASN cc_start: 0.7907 (m110) cc_final: 0.7672 (m110) REVERT: G 21 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5756 (tmt) REVERT: S 19 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8653 (tttm) REVERT: S 89 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: S 215 THR cc_start: 0.8366 (m) cc_final: 0.7973 (p) REVERT: R 56 MET cc_start: 0.7674 (mtm) cc_final: 0.7431 (mtt) REVERT: R 90 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7924 (mt) REVERT: R 149 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7812 (m) REVERT: R 153 VAL cc_start: 0.8350 (t) cc_final: 0.8099 (m) REVERT: R 194 TYR cc_start: 0.5798 (m-80) cc_final: 0.4382 (p90) outliers start: 29 outliers final: 10 residues processed: 144 average time/residue: 0.5165 time to fit residues: 79.9053 Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 365 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.159026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117431 restraints weight = 10104.587| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.63 r_work: 0.2941 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9246 Z= 0.104 Angle : 0.474 5.701 12535 Z= 0.249 Chirality : 0.039 0.136 1409 Planarity : 0.003 0.035 1577 Dihedral : 5.240 59.750 1325 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.07 % Allowed : 15.47 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.25), residues: 1129 helix: 3.00 (0.24), residues: 424 sheet: 1.09 (0.30), residues: 281 loop : 0.04 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.012 0.001 TYR S 190 PHE 0.015 0.001 PHE R 192 TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9242) covalent geometry : angle 0.47289 (12527) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.10873 ( 8) hydrogen bonds : bond 0.03862 ( 476) hydrogen bonds : angle 4.00182 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.336 Fit side-chains REVERT: A 17 LYS cc_start: 0.8030 (mttt) cc_final: 0.7745 (mtmm) REVERT: A 28 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7283 (pt0) REVERT: A 48 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8462 (t) REVERT: A 248 LYS cc_start: 0.8123 (mttt) cc_final: 0.7475 (mptp) REVERT: A 275 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7624 (mt-10) REVERT: A 298 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7098 (pt0) REVERT: B 22 ARG cc_start: 0.7359 (mtt180) cc_final: 0.7047 (mtt180) REVERT: B 217 MET cc_start: 0.7312 (ptt) cc_final: 0.6891 (pmm) REVERT: B 221 THR cc_start: 0.8777 (m) cc_final: 0.8437 (m) REVERT: B 223 THR cc_start: 0.8224 (t) cc_final: 0.7814 (m) REVERT: B 293 ASN cc_start: 0.7884 (m110) cc_final: 0.7649 (m110) REVERT: G 21 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5958 (tmt) REVERT: S 19 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8647 (tttm) REVERT: S 89 GLU cc_start: 0.8185 (pp20) cc_final: 0.7827 (pp20) REVERT: S 215 THR cc_start: 0.8451 (m) cc_final: 0.8085 (p) REVERT: R 56 MET cc_start: 0.7761 (mtm) cc_final: 0.7546 (mtt) REVERT: R 60 VAL cc_start: 0.7760 (p) cc_final: 0.7500 (t) REVERT: R 90 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7947 (mt) REVERT: R 149 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7926 (m) REVERT: R 153 VAL cc_start: 0.8397 (t) cc_final: 0.8171 (m) REVERT: R 194 TYR cc_start: 0.5713 (m-80) cc_final: 0.4493 (p90) outliers start: 30 outliers final: 15 residues processed: 147 average time/residue: 0.5216 time to fit residues: 82.2337 Evaluate side-chains 144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 365 SER Chi-restraints excluded: chain R residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114472 restraints weight = 10120.753| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.83 r_work: 0.2870 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9246 Z= 0.165 Angle : 0.538 6.806 12535 Z= 0.281 Chirality : 0.041 0.142 1409 Planarity : 0.004 0.038 1577 Dihedral : 5.265 58.879 1325 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.18 % Allowed : 15.68 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1129 helix: 2.84 (0.24), residues: 422 sheet: 1.11 (0.30), residues: 279 loop : -0.07 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.015 0.001 TYR B 264 PHE 0.014 0.002 PHE B 199 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9242) covalent geometry : angle 0.53667 (12527) SS BOND : bond 0.00573 ( 4) SS BOND : angle 1.51845 ( 8) hydrogen bonds : bond 0.04635 ( 476) hydrogen bonds : angle 4.19707 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.343 Fit side-chains REVERT: A 17 LYS cc_start: 0.8013 (mttt) cc_final: 0.7649 (mtmm) REVERT: A 25 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 28 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7388 (pt0) REVERT: A 48 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8441 (t) REVERT: A 208 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7634 (ttm110) REVERT: A 248 LYS cc_start: 0.8378 (mttt) cc_final: 0.7715 (mptp) REVERT: A 273 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7914 (tp) REVERT: A 275 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7683 (mt-10) REVERT: B 217 MET cc_start: 0.7357 (ptt) cc_final: 0.6817 (pmm) REVERT: B 221 THR cc_start: 0.8844 (m) cc_final: 0.8530 (m) REVERT: B 223 THR cc_start: 0.8271 (t) cc_final: 0.7870 (m) REVERT: B 293 ASN cc_start: 0.8024 (m110) cc_final: 0.7781 (m110) REVERT: G 21 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5900 (tmt) REVERT: S 19 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8687 (tttm) REVERT: S 89 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: S 183 GLN cc_start: 0.8038 (mt0) cc_final: 0.7643 (mp10) REVERT: S 215 THR cc_start: 0.8472 (m) cc_final: 0.8059 (p) REVERT: R 149 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8095 (m) REVERT: R 153 VAL cc_start: 0.8509 (t) cc_final: 0.8304 (m) REVERT: R 194 TYR cc_start: 0.5994 (m-80) cc_final: 0.4381 (p90) REVERT: R 226 GLN cc_start: 0.8389 (tp40) cc_final: 0.8148 (mm110) REVERT: R 420 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.6155 (mmt180) outliers start: 31 outliers final: 17 residues processed: 149 average time/residue: 0.5236 time to fit residues: 83.7159 Evaluate side-chains 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 365 SER Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 420 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.157727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116237 restraints weight = 10072.373| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.75 r_work: 0.2925 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9246 Z= 0.108 Angle : 0.484 5.800 12535 Z= 0.254 Chirality : 0.039 0.134 1409 Planarity : 0.003 0.035 1577 Dihedral : 4.955 58.862 1325 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.66 % Allowed : 16.39 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.25), residues: 1129 helix: 3.01 (0.24), residues: 422 sheet: 1.09 (0.31), residues: 273 loop : -0.10 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.012 0.001 TYR S 190 PHE 0.015 0.001 PHE R 192 TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9242) covalent geometry : angle 0.48317 (12527) SS BOND : bond 0.00447 ( 4) SS BOND : angle 1.20718 ( 8) hydrogen bonds : bond 0.03989 ( 476) hydrogen bonds : angle 4.09747 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.377 Fit side-chains REVERT: A 17 LYS cc_start: 0.8025 (mttt) cc_final: 0.7756 (mtmm) REVERT: A 25 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 28 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7373 (pt0) REVERT: A 48 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8459 (t) REVERT: A 248 LYS cc_start: 0.8272 (mttt) cc_final: 0.7645 (mptp) REVERT: A 298 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7134 (pt0) REVERT: B 181 THR cc_start: 0.8594 (p) cc_final: 0.8386 (m) REVERT: B 217 MET cc_start: 0.7322 (ptt) cc_final: 0.6859 (pmm) REVERT: B 221 THR cc_start: 0.8808 (m) cc_final: 0.8482 (m) REVERT: B 223 THR cc_start: 0.8275 (t) cc_final: 0.7878 (m) REVERT: B 293 ASN cc_start: 0.7944 (m110) cc_final: 0.7722 (m110) REVERT: G 21 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5909 (tmt) REVERT: S 19 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8672 (tttm) REVERT: S 89 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7823 (pp20) REVERT: S 213 THR cc_start: 0.8633 (m) cc_final: 0.8338 (p) REVERT: S 215 THR cc_start: 0.8473 (m) cc_final: 0.8058 (p) REVERT: R 60 VAL cc_start: 0.7878 (p) cc_final: 0.7626 (t) REVERT: R 149 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8104 (m) REVERT: R 153 VAL cc_start: 0.8511 (t) cc_final: 0.8302 (m) REVERT: R 194 TYR cc_start: 0.5892 (m-80) cc_final: 0.4535 (p90) REVERT: R 226 GLN cc_start: 0.8388 (tp40) cc_final: 0.8147 (mm110) outliers start: 26 outliers final: 14 residues processed: 145 average time/residue: 0.5259 time to fit residues: 82.0504 Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116449 restraints weight = 10107.407| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.63 r_work: 0.2936 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9246 Z= 0.110 Angle : 0.488 5.724 12535 Z= 0.256 Chirality : 0.040 0.297 1409 Planarity : 0.003 0.037 1577 Dihedral : 4.791 58.544 1325 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.56 % Allowed : 17.11 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1129 helix: 3.02 (0.24), residues: 422 sheet: 1.09 (0.31), residues: 273 loop : -0.14 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.012 0.001 TYR S 190 PHE 0.014 0.001 PHE R 192 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9242) covalent geometry : angle 0.48681 (12527) SS BOND : bond 0.00476 ( 4) SS BOND : angle 1.27248 ( 8) hydrogen bonds : bond 0.03935 ( 476) hydrogen bonds : angle 4.05956 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8030 (mttt) cc_final: 0.7762 (mtmm) REVERT: A 25 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: A 28 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7397 (pt0) REVERT: A 48 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 248 LYS cc_start: 0.8296 (mttt) cc_final: 0.7671 (mptp) REVERT: A 298 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7116 (pt0) REVERT: B 181 THR cc_start: 0.8600 (p) cc_final: 0.8386 (m) REVERT: B 221 THR cc_start: 0.8812 (m) cc_final: 0.8482 (m) REVERT: B 223 THR cc_start: 0.8297 (t) cc_final: 0.7895 (m) REVERT: B 293 ASN cc_start: 0.7937 (m110) cc_final: 0.7708 (m110) REVERT: G 21 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5896 (tmt) REVERT: S 19 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8623 (tttm) REVERT: S 89 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: S 183 GLN cc_start: 0.8026 (mt0) cc_final: 0.7587 (mp10) REVERT: S 213 THR cc_start: 0.8637 (m) cc_final: 0.8348 (p) REVERT: S 215 THR cc_start: 0.8464 (m) cc_final: 0.8053 (p) REVERT: R 60 VAL cc_start: 0.7805 (p) cc_final: 0.7563 (t) REVERT: R 149 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8107 (m) REVERT: R 194 TYR cc_start: 0.5933 (m-80) cc_final: 0.4515 (p90) REVERT: R 226 GLN cc_start: 0.8402 (tp40) cc_final: 0.8162 (mm110) REVERT: R 420 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5980 (mmt180) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 0.5441 time to fit residues: 84.2840 Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 365 SER Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 420 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117013 restraints weight = 10058.693| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.72 r_work: 0.2931 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9246 Z= 0.106 Angle : 0.482 5.611 12535 Z= 0.253 Chirality : 0.040 0.280 1409 Planarity : 0.003 0.038 1577 Dihedral : 4.664 58.480 1325 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.46 % Allowed : 17.01 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1129 helix: 2.99 (0.24), residues: 422 sheet: 1.03 (0.31), residues: 275 loop : -0.13 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 151 TYR 0.012 0.001 TYR S 190 PHE 0.014 0.001 PHE R 192 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9242) covalent geometry : angle 0.48154 (12527) SS BOND : bond 0.00463 ( 4) SS BOND : angle 1.27370 ( 8) hydrogen bonds : bond 0.03837 ( 476) hydrogen bonds : angle 4.03234 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.337 Fit side-chains REVERT: A 17 LYS cc_start: 0.8017 (mttt) cc_final: 0.7741 (mtmm) REVERT: A 25 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: A 28 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7375 (pt0) REVERT: A 48 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8449 (t) REVERT: A 248 LYS cc_start: 0.8261 (mttt) cc_final: 0.7631 (mptp) REVERT: A 272 ASP cc_start: 0.8126 (p0) cc_final: 0.7329 (p0) REVERT: A 298 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7109 (pt0) REVERT: B 19 ARG cc_start: 0.6194 (ttp-110) cc_final: 0.5759 (ttm-80) REVERT: B 22 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6797 (mtt180) REVERT: B 181 THR cc_start: 0.8643 (p) cc_final: 0.8436 (m) REVERT: B 221 THR cc_start: 0.8802 (m) cc_final: 0.8479 (m) REVERT: B 223 THR cc_start: 0.8297 (t) cc_final: 0.7898 (m) REVERT: B 258 ASP cc_start: 0.7625 (t0) cc_final: 0.7349 (t0) REVERT: B 293 ASN cc_start: 0.7927 (m110) cc_final: 0.7695 (m110) REVERT: G 21 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5873 (tmt) REVERT: S 19 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8582 (tttm) REVERT: S 46 GLU cc_start: 0.8313 (tt0) cc_final: 0.7975 (mt-10) REVERT: S 89 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: S 139 VAL cc_start: 0.8952 (p) cc_final: 0.8654 (t) REVERT: S 183 GLN cc_start: 0.8015 (mt0) cc_final: 0.7556 (mp10) REVERT: S 213 THR cc_start: 0.8625 (m) cc_final: 0.8332 (p) REVERT: S 215 THR cc_start: 0.8452 (m) cc_final: 0.8042 (p) REVERT: R 60 VAL cc_start: 0.7812 (p) cc_final: 0.7573 (t) REVERT: R 193 PHE cc_start: 0.6226 (m-80) cc_final: 0.5709 (m-80) REVERT: R 194 TYR cc_start: 0.5946 (m-80) cc_final: 0.4566 (p90) REVERT: R 226 GLN cc_start: 0.8386 (tp40) cc_final: 0.8144 (mm110) REVERT: R 420 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5957 (mmt180) outliers start: 24 outliers final: 15 residues processed: 147 average time/residue: 0.5182 time to fit residues: 82.0885 Evaluate side-chains 144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 365 SER Chi-restraints excluded: chain R residue 420 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.156148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114323 restraints weight = 9966.267| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.71 r_work: 0.2887 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9246 Z= 0.142 Angle : 0.528 7.750 12535 Z= 0.275 Chirality : 0.041 0.278 1409 Planarity : 0.004 0.043 1577 Dihedral : 4.778 58.016 1325 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.56 % Allowed : 17.52 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1129 helix: 2.87 (0.24), residues: 422 sheet: 1.05 (0.31), residues: 273 loop : -0.21 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.015 0.001 TYR B 264 PHE 0.013 0.001 PHE B 199 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9242) covalent geometry : angle 0.52723 (12527) SS BOND : bond 0.00588 ( 4) SS BOND : angle 1.51036 ( 8) hydrogen bonds : bond 0.04327 ( 476) hydrogen bonds : angle 4.13243 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3210.23 seconds wall clock time: 55 minutes 10.65 seconds (3310.65 seconds total)