Starting phenix.real_space_refine on Thu Jul 2 13:50:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrq_39549/07_2026/8yrq_39549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrq_39549/07_2026/8yrq_39549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yrq_39549/07_2026/8yrq_39549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrq_39549/07_2026/8yrq_39549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yrq_39549/07_2026/8yrq_39549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrq_39549/07_2026/8yrq_39549.map" } resolution = 2.8 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= 0.002 sd= 0.059 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 57 5.16 5 C 5508 2.51 5 N 1486 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8672 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2201 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 285} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1675 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 419 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 1.79, per 1000 atoms: 0.21 Number of scatterers: 8672 At special positions: 0 Unit cell: (88.35, 118.11, 128.34, 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 57 16.00 O 1621 8.00 N 1486 7.00 C 5508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 149 " - pdb=" SG CYS R 228 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 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: 0.49 Conformation dependent library (CDL) restraints added in 434.4 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 36.3% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 64 through 72 removed outlier: 3.957A pdb=" N LEU R 70 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU R 71 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 104 removed outlier: 3.945A pdb=" N LEU R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL R 80 " --> pdb=" O PRO R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix removed outlier: 3.857A pdb=" N LEU R 88 " --> pdb=" O TYR R 84 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 109 through 128 removed outlier: 3.753A pdb=" N LEU R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 136 removed outlier: 4.216A pdb=" N ARG R 132 " --> pdb=" O ALA R 128 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 134 " --> pdb=" O PRO R 130 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR R 135 " --> pdb=" O PRO R 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 180 removed outlier: 3.593A pdb=" N TYR R 161 " --> pdb=" O TYR R 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL R 164 " --> pdb=" O MET R 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP R 165 " --> pdb=" O TYR R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 209 Processing helix chain 'R' and resid 210 through 213 Processing helix chain 'R' and resid 234 through 240 Processing helix chain 'R' and resid 240 through 253 removed outlier: 3.764A pdb=" N THR R 246 " --> pdb=" O GLN R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 272 Processing helix chain 'R' and resid 273 through 275 No H-bonds generated for 'chain 'R' and resid 273 through 275' Processing helix chain 'R' and resid 281 through 307 removed outlier: 3.751A pdb=" N ALA R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL R 287 " --> pdb=" O ARG R 283 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 318 through 331 Proline residue: R 324 - end of helix removed outlier: 3.656A pdb=" N ALA R 327 " --> pdb=" O VAL R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 347 through 353 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.813A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.927A pdb=" N ILE A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.589A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 44 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: 4.024A 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 removed outlier: 3.545A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 61 through 62 removed outlier: 5.071A pdb=" N TYR R 49 " --> pdb=" O LEU R 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 218 through 219 Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 192 removed outlier: 9.465A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.369A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.635A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.151A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.220A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.671A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.587A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.488A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.539A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.114A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.772A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1194 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: 1.08 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2820 1.34 - 1.46: 2003 1.46 - 1.58: 3954 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8859 Sorted by residual: bond pdb=" N SER R 344 " pdb=" CA SER R 344 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.91e+00 bond pdb=" C GLU S 222 " pdb=" N TYR S 223 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.83e-02 1.25e+03 5.88e+00 bond pdb=" N VAL R 351 " pdb=" CA VAL R 351 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.29e+00 bond pdb=" N ARG R 352 " pdb=" CA ARG R 352 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.86e+00 bond pdb=" N LYS R 350 " pdb=" CA LYS R 350 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.30e-02 5.92e+03 3.91e+00 ... (remaining 8854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11644 1.80 - 3.59: 331 3.59 - 5.39: 50 5.39 - 7.19: 14 7.19 - 8.99: 4 Bond angle restraints: 12043 Sorted by residual: angle pdb=" CA TYR R 341 " pdb=" C TYR R 341 " pdb=" N TYR R 342 " ideal model delta sigma weight residual 118.39 110.99 7.40 1.38e+00 5.25e-01 2.88e+01 angle pdb=" N ASP R 349 " pdb=" CA ASP R 349 " pdb=" C ASP R 349 " ideal model delta sigma weight residual 111.36 105.64 5.72 1.09e+00 8.42e-01 2.76e+01 angle pdb=" N LYS R 350 " pdb=" CA LYS R 350 " pdb=" C LYS R 350 " ideal model delta sigma weight residual 112.38 106.01 6.37 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N VAL R 351 " pdb=" CA VAL R 351 " pdb=" C VAL R 351 " ideal model delta sigma weight residual 111.00 105.85 5.15 1.09e+00 8.42e-01 2.23e+01 angle pdb=" N ARG R 348 " pdb=" CA ARG R 348 " pdb=" C ARG R 348 " ideal model delta sigma weight residual 112.38 106.80 5.58 1.22e+00 6.72e-01 2.09e+01 ... (remaining 12038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4855 17.92 - 35.83: 341 35.83 - 53.75: 47 53.75 - 71.66: 9 71.66 - 89.58: 4 Dihedral angle restraints: 5256 sinusoidal: 1960 harmonic: 3296 Sorted by residual: dihedral pdb=" CA TYR A 231 " pdb=" C TYR A 231 " pdb=" N ASN A 242 " pdb=" CA ASN A 242 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N GLY B 77 " pdb=" CA GLY B 77 " ideal model delta harmonic sigma weight residual 180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 934 0.041 - 0.081: 315 0.081 - 0.122: 109 0.122 - 0.162: 15 0.162 - 0.203: 7 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA VAL R 351 " pdb=" N VAL R 351 " pdb=" C VAL R 351 " pdb=" CB VAL R 351 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 1377 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 341 " -0.023 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C TYR R 341 " 0.086 2.00e-02 2.50e+03 pdb=" O TYR R 341 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR R 342 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO G 55 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 236 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 179 2.66 - 3.22: 8306 3.22 - 3.78: 14065 3.78 - 4.34: 19744 4.34 - 4.90: 32535 Nonbonded interactions: 74829 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.106 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.111 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.218 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.222 3.040 nonbonded pdb=" O CYS A 255 " pdb=" NZ LYS A 317 " model vdw 2.225 3.120 ... (remaining 74824 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: 0.930 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.040 Find NCS groups from input model: 0.030 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.006 0.069 8862 Z= 0.249 Angle : 0.743 8.985 12049 Z= 0.423 Chirality : 0.047 0.203 1380 Planarity : 0.005 0.050 1536 Dihedral : 12.562 89.577 3125 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 0.11 % Allowed : 0.44 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.90 (0.25), residues: 1124 helix: 0.34 (0.29), residues: 354 sheet: -0.67 (0.28), residues: 286 loop : -1.16 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 251 TYR 0.032 0.002 TYR A 320 PHE 0.014 0.002 PHE B 235 TRP 0.032 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 ( 8859) covalent geometry : angle 0.74264 / 0.42 (12043) SS BOND : bond 0.00089 / 0.05 ( 3) SS BOND : angle 1.55418 / 0.72 ( 6) hydrogen bonds : bond 0.14195 / 10.07 ( 424) hydrogen bonds : angle 6.99869 / 5.10 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.351 Fit side-chains REVERT: G 22 GLU cc_start: 0.8547 (tt0) cc_final: 0.8285 (tt0) outliers start: 1 outliers final: 2 residues processed: 219 average time/residue: 0.4809 time to fit residues: 112.0076 Evaluate side-chains 148 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 136 HIS ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN A 322 HIS B 44 GLN B 156 GLN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.135095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089295 restraints weight = 12795.266| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.79 r_work: 0.3031 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8862 Z= 0.210 Angle : 0.701 10.534 12049 Z= 0.347 Chirality : 0.046 0.175 1380 Planarity : 0.005 0.052 1536 Dihedral : 5.187 57.433 1235 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.39 % Allowed : 13.13 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.55 (0.25), residues: 1124 helix: 0.80 (0.28), residues: 366 sheet: -0.58 (0.29), residues: 281 loop : -1.07 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.017 0.002 TYR B 59 PHE 0.021 0.002 PHE R 347 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 8859) covalent geometry : angle 0.70039 / 0.35 (12043) SS BOND : bond 0.00163 / 0.08 ( 3) SS BOND : angle 1.37619 / 0.65 ( 6) hydrogen bonds : bond 0.03933 / 2.71 ( 424) hydrogen bonds : angle 5.57713 / 4.12 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 THR cc_start: 0.8444 (m) cc_final: 0.8226 (p) REVERT: A 18 MET cc_start: 0.8709 (mtp) cc_final: 0.8451 (mtp) REVERT: A 272 LYS cc_start: 0.7946 (tptt) cc_final: 0.7709 (ttmt) REVERT: B 17 GLN cc_start: 0.8959 (tp40) cc_final: 0.8664 (tp40) REVERT: B 245 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8233 (t) REVERT: G 58 GLU cc_start: 0.8149 (pm20) cc_final: 0.7920 (pm20) REVERT: S 93 MET cc_start: 0.8964 (ttt) cc_final: 0.8606 (ttp) REVERT: S 141 GLU cc_start: 0.8360 (pt0) cc_final: 0.8150 (pt0) REVERT: S 146 SER cc_start: 0.8987 (m) cc_final: 0.8712 (p) REVERT: S 208 GLU cc_start: 0.8271 (pt0) cc_final: 0.7807 (pp20) outliers start: 31 outliers final: 10 residues processed: 177 average time/residue: 0.5251 time to fit residues: 98.7584 Evaluate side-chains 149 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 136 HIS R 300 ASN A 322 HIS B 75 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088844 restraints weight = 12615.355| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.78 r_work: 0.3029 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8862 Z= 0.185 Angle : 0.629 9.423 12049 Z= 0.314 Chirality : 0.043 0.170 1380 Planarity : 0.005 0.049 1536 Dihedral : 4.617 22.688 1230 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.94 % Allowed : 15.54 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.43 (0.26), residues: 1124 helix: 1.04 (0.28), residues: 367 sheet: -0.54 (0.29), residues: 285 loop : -1.11 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.012 0.002 TYR B 59 PHE 0.014 0.001 PHE R 347 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 8859) covalent geometry : angle 0.62896 / 0.31 (12043) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 1.28009 / 0.61 ( 6) hydrogen bonds : bond 0.03636 / 2.51 ( 424) hydrogen bonds : angle 5.30792 / 3.92 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8092 (ppp) cc_final: 0.7869 (ppp) REVERT: R 116 MET cc_start: 0.8294 (mtm) cc_final: 0.8063 (mtt) REVERT: R 230 ASP cc_start: 0.6471 (t0) cc_final: 0.6265 (t0) REVERT: A 272 LYS cc_start: 0.7972 (tptt) cc_final: 0.7712 (ttmt) REVERT: B 15 LYS cc_start: 0.9345 (mtpp) cc_final: 0.8907 (tmmt) REVERT: B 17 GLN cc_start: 0.9033 (tp40) cc_final: 0.8826 (tp40) REVERT: B 19 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8059 (ttp-110) REVERT: B 172 GLU cc_start: 0.8685 (tp30) cc_final: 0.8481 (tp30) REVERT: B 195 ASP cc_start: 0.8974 (p0) cc_final: 0.8732 (p0) REVERT: B 245 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8247 (t) REVERT: G 58 GLU cc_start: 0.8050 (pm20) cc_final: 0.7764 (pm20) REVERT: S 87 ARG cc_start: 0.7532 (mpp80) cc_final: 0.7326 (mtt90) REVERT: S 141 GLU cc_start: 0.8405 (pt0) cc_final: 0.8160 (pt0) REVERT: S 146 SER cc_start: 0.9001 (m) cc_final: 0.8765 (p) REVERT: S 167 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8964 (tt0) REVERT: S 208 GLU cc_start: 0.8227 (pt0) cc_final: 0.7921 (pp20) outliers start: 36 outliers final: 19 residues processed: 168 average time/residue: 0.5098 time to fit residues: 91.0005 Evaluate side-chains 158 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 1 optimal weight: 0.0070 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 136 HIS A 322 HIS B 75 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089396 restraints weight = 12853.056| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.72 r_work: 0.3038 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8862 Z= 0.166 Angle : 0.619 8.534 12049 Z= 0.307 Chirality : 0.043 0.181 1380 Planarity : 0.005 0.058 1536 Dihedral : 4.533 23.133 1230 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.83 % Allowed : 16.52 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.36 (0.26), residues: 1124 helix: 1.17 (0.28), residues: 366 sheet: -0.54 (0.29), residues: 287 loop : -1.11 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 96 TYR 0.013 0.001 TYR S 178 PHE 0.011 0.001 PHE A 190 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 8859) covalent geometry : angle 0.61860 / 0.31 (12043) SS BOND : bond 0.00053 / 0.03 ( 3) SS BOND : angle 1.15209 / 0.55 ( 6) hydrogen bonds : bond 0.03422 / 2.36 ( 424) hydrogen bonds : angle 5.12992 / 3.79 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8037 (ppp) cc_final: 0.7804 (ppp) REVERT: R 116 MET cc_start: 0.8293 (mtm) cc_final: 0.8023 (mtt) REVERT: R 230 ASP cc_start: 0.6313 (t0) cc_final: 0.6090 (t0) REVERT: B 40 VAL cc_start: 0.8959 (p) cc_final: 0.8715 (t) REVERT: B 172 GLU cc_start: 0.8742 (tp30) cc_final: 0.8525 (tp30) REVERT: G 58 GLU cc_start: 0.8188 (pm20) cc_final: 0.7981 (pm20) REVERT: S 76 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8551 (pttp) REVERT: S 141 GLU cc_start: 0.8423 (pt0) cc_final: 0.8151 (pt0) REVERT: S 146 SER cc_start: 0.9035 (m) cc_final: 0.8794 (p) REVERT: S 167 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8925 (tt0) REVERT: S 208 GLU cc_start: 0.8281 (pt0) cc_final: 0.7885 (pp20) outliers start: 35 outliers final: 18 residues processed: 167 average time/residue: 0.4898 time to fit residues: 87.0310 Evaluate side-chains 156 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 136 HIS R 300 ASN A 322 HIS B 75 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088735 restraints weight = 12809.948| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.80 r_work: 0.3023 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8862 Z= 0.168 Angle : 0.628 12.114 12049 Z= 0.308 Chirality : 0.043 0.179 1380 Planarity : 0.004 0.051 1536 Dihedral : 4.486 21.961 1230 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.27 % Allowed : 17.94 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.31 (0.26), residues: 1124 helix: 1.18 (0.28), residues: 373 sheet: -0.51 (0.29), residues: 294 loop : -1.10 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 96 TYR 0.013 0.001 TYR S 178 PHE 0.011 0.001 PHE A 190 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8859) covalent geometry : angle 0.62725 / 0.31 (12043) SS BOND : bond 0.00100 / 0.05 ( 3) SS BOND : angle 1.05551 / 0.50 ( 6) hydrogen bonds : bond 0.03300 / 2.28 ( 424) hydrogen bonds : angle 5.05626 / 3.73 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8060 (ppp) cc_final: 0.7786 (ppp) REVERT: R 116 MET cc_start: 0.8301 (mtm) cc_final: 0.8070 (mtt) REVERT: R 230 ASP cc_start: 0.6399 (t0) cc_final: 0.6134 (t0) REVERT: B 17 GLN cc_start: 0.9025 (tp40) cc_final: 0.8821 (tp40) REVERT: B 19 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8385 (ttp80) REVERT: G 52 THR cc_start: 0.7456 (p) cc_final: 0.7238 (p) REVERT: G 58 GLU cc_start: 0.8129 (pm20) cc_final: 0.7897 (pm20) REVERT: S 76 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8563 (pttt) REVERT: S 146 SER cc_start: 0.9073 (m) cc_final: 0.8836 (p) REVERT: S 167 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8929 (tt0) REVERT: S 208 GLU cc_start: 0.8279 (pt0) cc_final: 0.7963 (pp20) outliers start: 39 outliers final: 19 residues processed: 160 average time/residue: 0.4804 time to fit residues: 81.7977 Evaluate side-chains 152 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 196 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 300 ASN A 345 GLN B 75 GLN B 239 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090545 restraints weight = 12782.137| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.76 r_work: 0.3053 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8862 Z= 0.134 Angle : 0.621 10.698 12049 Z= 0.304 Chirality : 0.042 0.207 1380 Planarity : 0.005 0.069 1536 Dihedral : 4.385 21.579 1230 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.94 % Allowed : 18.27 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.19 (0.26), residues: 1124 helix: 1.30 (0.28), residues: 374 sheet: -0.40 (0.30), residues: 288 loop : -1.07 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 96 TYR 0.014 0.001 TYR S 178 PHE 0.010 0.001 PHE A 190 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8859) covalent geometry : angle 0.62055 / 0.30 (12043) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 1.01000 / 0.47 ( 6) hydrogen bonds : bond 0.03171 / 2.20 ( 424) hydrogen bonds : angle 4.97566 / 3.69 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8035 (ppp) cc_final: 0.7726 (ppp) REVERT: R 116 MET cc_start: 0.8283 (mtm) cc_final: 0.8057 (mtt) REVERT: A 210 LYS cc_start: 0.8895 (ptmt) cc_final: 0.8550 (pttm) REVERT: A 243 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8457 (mtp-110) REVERT: B 17 GLN cc_start: 0.9026 (tp40) cc_final: 0.8809 (tp40) REVERT: G 52 THR cc_start: 0.7358 (p) cc_final: 0.7147 (p) REVERT: G 58 GLU cc_start: 0.8070 (pm20) cc_final: 0.7825 (pm20) REVERT: S 76 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8501 (pttt) REVERT: S 89 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: S 141 GLU cc_start: 0.8557 (pt0) cc_final: 0.7961 (pm20) REVERT: S 146 SER cc_start: 0.9058 (m) cc_final: 0.8817 (p) REVERT: S 167 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: S 208 GLU cc_start: 0.8316 (pt0) cc_final: 0.7901 (pp20) outliers start: 36 outliers final: 19 residues processed: 167 average time/residue: 0.4509 time to fit residues: 80.1105 Evaluate side-chains 154 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 198 MET Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 196 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090398 restraints weight = 12892.860| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.83 r_work: 0.3058 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8862 Z= 0.134 Angle : 0.603 10.155 12049 Z= 0.299 Chirality : 0.042 0.179 1380 Planarity : 0.004 0.051 1536 Dihedral : 4.266 21.099 1230 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.28 % Allowed : 19.37 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.11 (0.26), residues: 1124 helix: 1.37 (0.29), residues: 373 sheet: -0.41 (0.30), residues: 288 loop : -0.99 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 96 TYR 0.014 0.001 TYR R 84 PHE 0.010 0.001 PHE A 190 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 8859) covalent geometry : angle 0.60238 / 0.30 (12043) SS BOND : bond 0.00097 / 0.05 ( 3) SS BOND : angle 0.91915 / 0.43 ( 6) hydrogen bonds : bond 0.03109 / 2.16 ( 424) hydrogen bonds : angle 4.89820 / 3.62 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8043 (ppp) cc_final: 0.7749 (ppp) REVERT: R 116 MET cc_start: 0.8314 (mtm) cc_final: 0.8087 (mtt) REVERT: A 210 LYS cc_start: 0.8875 (ptmt) cc_final: 0.8566 (pttm) REVERT: B 19 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8373 (ttp80) REVERT: B 215 GLU cc_start: 0.8776 (mp0) cc_final: 0.8410 (mp0) REVERT: G 52 THR cc_start: 0.7464 (p) cc_final: 0.7261 (p) REVERT: S 76 LYS cc_start: 0.8777 (ptpp) cc_final: 0.8420 (pttt) REVERT: S 89 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: S 141 GLU cc_start: 0.8592 (pt0) cc_final: 0.8295 (pt0) REVERT: S 146 SER cc_start: 0.8995 (m) cc_final: 0.8774 (p) REVERT: S 167 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: S 208 GLU cc_start: 0.8163 (pt0) cc_final: 0.7899 (pp20) outliers start: 30 outliers final: 17 residues processed: 171 average time/residue: 0.4803 time to fit residues: 87.6358 Evaluate side-chains 156 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 198 MET Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 196 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN A 345 GLN B 75 GLN B 175 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088378 restraints weight = 12743.330| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.78 r_work: 0.3025 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8862 Z= 0.195 Angle : 0.658 9.876 12049 Z= 0.325 Chirality : 0.044 0.178 1380 Planarity : 0.005 0.052 1536 Dihedral : 4.426 19.874 1230 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.06 % Allowed : 20.35 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.16 (0.26), residues: 1124 helix: 1.32 (0.28), residues: 372 sheet: -0.47 (0.29), residues: 291 loop : -0.98 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.014 0.001 TYR A 297 PHE 0.011 0.001 PHE A 190 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 8859) covalent geometry : angle 0.65477 / 0.32 (12043) SS BOND : bond 0.00139 / 0.08 ( 3) SS BOND : angle 3.17950 / 2.12 ( 6) hydrogen bonds : bond 0.03342 / 2.30 ( 424) hydrogen bonds : angle 4.95843 / 3.67 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8055 (ppp) cc_final: 0.7763 (ppp) REVERT: R 116 MET cc_start: 0.8352 (mtm) cc_final: 0.8128 (mtt) REVERT: R 309 ASP cc_start: 0.6733 (m-30) cc_final: 0.6274 (m-30) REVERT: R 328 LEU cc_start: 0.8223 (mp) cc_final: 0.7766 (tt) REVERT: A 210 LYS cc_start: 0.8896 (ptmt) cc_final: 0.8572 (pttm) REVERT: B 19 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8388 (ttp80) REVERT: B 175 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8142 (OUTLIER) REVERT: B 215 GLU cc_start: 0.8888 (mp0) cc_final: 0.8412 (mp0) REVERT: G 48 ASP cc_start: 0.8393 (t0) cc_final: 0.8183 (t0) REVERT: G 52 THR cc_start: 0.7517 (p) cc_final: 0.7306 (p) REVERT: S 76 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8510 (pttt) REVERT: S 89 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: S 141 GLU cc_start: 0.8571 (pt0) cc_final: 0.8269 (pt0) REVERT: S 146 SER cc_start: 0.8986 (m) cc_final: 0.8724 (p) REVERT: S 167 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8949 (tt0) REVERT: S 208 GLU cc_start: 0.8357 (pt0) cc_final: 0.7801 (pp20) REVERT: S 211 ASP cc_start: 0.9298 (m-30) cc_final: 0.8403 (m-30) outliers start: 28 outliers final: 18 residues processed: 154 average time/residue: 0.4859 time to fit residues: 79.6283 Evaluate side-chains 154 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 196 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.3980 chunk 92 optimal weight: 0.0040 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN B 75 GLN B 175 GLN B 237 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.135739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090952 restraints weight = 12824.384| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.81 r_work: 0.3073 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8862 Z= 0.126 Angle : 0.630 9.585 12049 Z= 0.314 Chirality : 0.042 0.179 1380 Planarity : 0.004 0.053 1536 Dihedral : 4.310 19.366 1230 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.84 % Allowed : 21.33 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.03 (0.26), residues: 1124 helix: 1.42 (0.29), residues: 372 sheet: -0.35 (0.30), residues: 283 loop : -0.93 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.013 0.001 TYR S 178 PHE 0.013 0.001 PHE R 218 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8859) covalent geometry : angle 0.62747 / 0.31 (12043) SS BOND : bond 0.00169 / 0.09 ( 3) SS BOND : angle 2.64554 / 1.76 ( 6) hydrogen bonds : bond 0.03091 / 2.14 ( 424) hydrogen bonds : angle 4.86997 / 3.62 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.8039 (ppp) cc_final: 0.7739 (ppp) REVERT: R 116 MET cc_start: 0.8312 (mtm) cc_final: 0.8067 (mtt) REVERT: R 309 ASP cc_start: 0.6726 (m-30) cc_final: 0.6237 (m-30) REVERT: R 328 LEU cc_start: 0.8163 (mp) cc_final: 0.7731 (tt) REVERT: A 210 LYS cc_start: 0.8861 (ptmt) cc_final: 0.8550 (pttm) REVERT: B 19 ARG cc_start: 0.8631 (ttm110) cc_final: 0.8394 (ttp80) REVERT: B 175 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7977 (OUTLIER) REVERT: B 215 GLU cc_start: 0.8830 (mp0) cc_final: 0.8385 (mp0) REVERT: G 52 THR cc_start: 0.7513 (p) cc_final: 0.7299 (p) REVERT: S 76 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8422 (pttt) REVERT: S 89 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: S 141 GLU cc_start: 0.8609 (pt0) cc_final: 0.8291 (pt0) REVERT: S 146 SER cc_start: 0.8962 (m) cc_final: 0.8662 (p) REVERT: S 167 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8804 (tt0) REVERT: S 208 GLU cc_start: 0.8268 (pt0) cc_final: 0.7900 (pp20) outliers start: 26 outliers final: 18 residues processed: 159 average time/residue: 0.5078 time to fit residues: 86.0447 Evaluate side-chains 162 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 37 optimal weight: 0.0020 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN B 75 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.092424 restraints weight = 12843.239| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.77 r_work: 0.3089 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8862 Z= 0.123 Angle : 0.646 9.985 12049 Z= 0.318 Chirality : 0.042 0.186 1380 Planarity : 0.004 0.053 1536 Dihedral : 4.245 18.797 1230 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.19 % Allowed : 22.21 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.04 (0.26), residues: 1124 helix: 1.41 (0.29), residues: 372 sheet: -0.28 (0.30), residues: 281 loop : -0.98 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.013 0.001 TYR S 178 PHE 0.011 0.001 PHE R 218 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8859) covalent geometry : angle 0.64374 / 0.32 (12043) SS BOND : bond 0.00183 / 0.10 ( 3) SS BOND : angle 2.61669 / 1.74 ( 6) hydrogen bonds : bond 0.03015 / 2.09 ( 424) hydrogen bonds : angle 4.81517 / 3.58 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 113 MET cc_start: 0.7999 (ppp) cc_final: 0.7704 (ppp) REVERT: R 116 MET cc_start: 0.8228 (mtm) cc_final: 0.7950 (mtt) REVERT: R 328 LEU cc_start: 0.8092 (mp) cc_final: 0.7687 (tt) REVERT: A 210 LYS cc_start: 0.8845 (ptmt) cc_final: 0.8517 (pttm) REVERT: A 231 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6684 (p90) REVERT: B 16 ASN cc_start: 0.8906 (m-40) cc_final: 0.8638 (m-40) REVERT: B 19 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8373 (ttp80) REVERT: B 175 GLN cc_start: 0.8076 (pp30) cc_final: 0.7841 (OUTLIER) REVERT: B 215 GLU cc_start: 0.8834 (mp0) cc_final: 0.8380 (mp0) REVERT: G 52 THR cc_start: 0.7386 (p) cc_final: 0.7183 (p) REVERT: S 76 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8416 (pttt) REVERT: S 89 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: S 141 GLU cc_start: 0.8605 (pt0) cc_final: 0.8287 (pt0) REVERT: S 146 SER cc_start: 0.8975 (m) cc_final: 0.8675 (p) REVERT: S 167 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: S 208 GLU cc_start: 0.8163 (pt0) cc_final: 0.7819 (pp20) outliers start: 20 outliers final: 16 residues processed: 157 average time/residue: 0.4847 time to fit residues: 81.1672 Evaluate side-chains 158 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 59 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN B 75 GLN B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092130 restraints weight = 12782.035| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.75 r_work: 0.3085 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8862 Z= 0.131 Angle : 0.639 9.364 12049 Z= 0.314 Chirality : 0.043 0.210 1380 Planarity : 0.004 0.049 1536 Dihedral : 4.204 18.812 1230 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 22.10 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.00 (0.26), residues: 1124 helix: 1.42 (0.29), residues: 372 sheet: -0.23 (0.30), residues: 281 loop : -0.96 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.013 0.001 TYR S 178 PHE 0.010 0.001 PHE G 61 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8859) covalent geometry : angle 0.63664 / 0.31 (12043) SS BOND : bond 0.00201 / 0.11 ( 3) SS BOND : angle 2.53733 / 1.68 ( 6) hydrogen bonds : bond 0.03033 / 2.10 ( 424) hydrogen bonds : angle 4.79766 / 3.56 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.86 seconds wall clock time: 55 minutes 21.85 seconds (3321.85 seconds total)