Starting phenix.real_space_refine on Thu Jul 2 10:56:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmp_34902/07_2026/8hmp_34902.map" } resolution = 2.77 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5294 2.51 5 N 1433 2.21 5 O 1532 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 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: 8319 Number of models: 1 Model: "" Number of chains: 6 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: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2308 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "A" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1980 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EN6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.20 Number of scatterers: 8319 At special positions: 0 Unit cell: (94.8486, 94.2939, 125.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 3 9.00 O 1532 8.00 N 1433 7.00 C 5294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS R 40 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 193 " distance=2.02 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: 0.52 Conformation dependent library (CDL) restraints added in 326.5 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 40.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.642A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.568A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 68 removed outlier: 4.063A pdb=" N VAL R 46 " --> pdb=" O PHE R 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS R 66 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 104 removed outlier: 3.901A pdb=" N PHE R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) Proline residue: R 97 - end of helix removed outlier: 4.254A pdb=" N LEU R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 145 removed outlier: 3.739A pdb=" N THR R 113 " --> pdb=" O HIS R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 153 Processing helix chain 'R' and resid 154 through 174 removed outlier: 3.720A pdb=" N PHE R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.797A pdb=" N PHE R 178 " --> pdb=" O LEU R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 189 removed outlier: 4.006A pdb=" N ILE R 189 " --> pdb=" O HIS R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 196 removed outlier: 3.636A pdb=" N ALA R 194 " --> pdb=" O PHE R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 244 Proline residue: R 214 - end of helix Processing helix chain 'R' and resid 263 through 289 removed outlier: 4.284A pdb=" N LEU R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE R 268 " --> pdb=" O ALA R 264 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG R 269 " --> pdb=" O MET R 265 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Proline residue: R 280 - end of helix Processing helix chain 'R' and resid 295 through 309 Processing helix chain 'R' and resid 311 through 321 removed outlier: 3.613A pdb=" N TYR R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER R 320 " --> pdb=" O ILE R 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.506A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.507A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.330A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.606A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.875A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.686A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.995A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.044A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.633A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.506A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.795A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.192A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1182 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: 1.12 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2510 1.34 - 1.46: 2252 1.46 - 1.59: 3671 1.59 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8509 Sorted by residual: bond pdb=" C1 EN6 R 401 " pdb=" N1 EN6 R 401 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C22 EN6 R 401 " pdb=" N3 EN6 R 401 " ideal model delta sigma weight residual 1.344 1.442 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C17 EN6 R 401 " pdb=" C18 EN6 R 401 " ideal model delta sigma weight residual 1.381 1.435 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" C17 EN6 R 401 " pdb=" N1 EN6 R 401 " ideal model delta sigma weight residual 1.356 1.406 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C18 EN6 R 401 " pdb=" C22 EN6 R 401 " ideal model delta sigma weight residual 1.479 1.525 -0.046 2.00e-02 2.50e+03 5.38e+00 ... (remaining 8504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 11373 3.14 - 6.29: 150 6.29 - 9.43: 14 9.43 - 12.57: 5 12.57 - 15.72: 1 Bond angle restraints: 11543 Sorted by residual: angle pdb=" CB MET R 276 " pdb=" CG MET R 276 " pdb=" SD MET R 276 " ideal model delta sigma weight residual 112.70 128.42 -15.72 3.00e+00 1.11e-01 2.74e+01 angle pdb=" C VAL R 64 " pdb=" N PHE R 65 " pdb=" CA PHE R 65 " ideal model delta sigma weight residual 120.58 112.87 7.71 1.71e+00 3.42e-01 2.03e+01 angle pdb=" N GLN R 115 " pdb=" CA GLN R 115 " pdb=" CB GLN R 115 " ideal model delta sigma weight residual 110.12 116.30 -6.18 1.47e+00 4.63e-01 1.76e+01 angle pdb=" CA GLN R 115 " pdb=" CB GLN R 115 " pdb=" CG GLN R 115 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" C HIS R 72 " pdb=" N HIS R 73 " pdb=" CA HIS R 73 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 11538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.41: 4829 27.41 - 54.82: 164 54.82 - 82.23: 26 82.23 - 109.64: 1 109.64 - 137.04: 1 Dihedral angle restraints: 5021 sinusoidal: 1975 harmonic: 3046 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -12.36 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual -86.00 -142.01 56.01 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 5018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 884 0.051 - 0.102: 295 0.102 - 0.153: 87 0.153 - 0.204: 16 0.204 - 0.255: 5 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA MET R 276 " pdb=" N MET R 276 " pdb=" C MET R 276 " pdb=" CB MET R 276 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU R 279 " pdb=" N LEU R 279 " pdb=" C LEU R 279 " pdb=" CB LEU R 279 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1284 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.034 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR B 59 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 244 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO R 245 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO R 245 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 245 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 278 " -0.018 2.00e-02 2.50e+03 1.96e-02 9.60e+00 pdb=" CG TRP R 278 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 278 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP R 278 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 278 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 278 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 278 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 278 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 278 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP R 278 " -0.000 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1275 2.76 - 3.30: 7980 3.30 - 3.83: 14436 3.83 - 4.37: 17191 4.37 - 4.90: 29413 Nonbonded interactions: 70295 Sorted by model distance: nonbonded pdb=" O THR R 199 " pdb=" OG SER R 290 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.240 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.318 3.040 ... (remaining 70290 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: 10.840 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: 0.250 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.005 0.100 8513 Z= 0.241 Angle : 0.919 15.717 11551 Z= 0.489 Chirality : 0.057 0.255 1287 Planarity : 0.006 0.088 1465 Dihedral : 14.091 137.044 3043 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1031 helix: 0.01 (0.25), residues: 390 sheet: 0.04 (0.31), residues: 232 loop : -1.16 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 291 TYR 0.062 0.003 TYR B 59 PHE 0.024 0.002 PHE N 108 TRP 0.049 0.003 TRP R 278 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 8509) covalent geometry : angle 0.91867 / 0.49 (11543) SS BOND : bond 0.00557 / 0.28 ( 4) SS BOND : angle 1.59977 / 0.80 ( 8) hydrogen bonds : bond 0.13521 / 9.26 ( 409) hydrogen bonds : angle 5.99898 / 4.21 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: N 73 ASP cc_start: 0.7515 (m-30) cc_final: 0.7017 (m-30) REVERT: N 80 TYR cc_start: 0.8167 (m-80) cc_final: 0.7628 (m-80) REVERT: R 190 PHE cc_start: 0.7995 (m-80) cc_final: 0.7732 (m-80) REVERT: R 198 LEU cc_start: 0.8008 (mt) cc_final: 0.7681 (mm) REVERT: R 200 SER cc_start: 0.7924 (p) cc_final: 0.7630 (p) REVERT: R 220 CYS cc_start: 0.7605 (m) cc_final: 0.7173 (m) REVERT: R 265 MET cc_start: 0.5522 (tmm) cc_final: 0.4651 (mtt) REVERT: A 307 LYS cc_start: 0.8154 (mppt) cc_final: 0.7895 (mmtm) REVERT: A 311 TYR cc_start: 0.8130 (m-80) cc_final: 0.7914 (m-80) REVERT: A 343 ASP cc_start: 0.7295 (m-30) cc_final: 0.6963 (m-30) REVERT: A 369 THR cc_start: 0.7789 (p) cc_final: 0.7573 (p) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.5242 time to fit residues: 135.3771 Evaluate side-chains 192 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 88 ASN B 266 HIS N 77 ASN R 81 GLN A 14 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.190147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149260 restraints weight = 9518.664| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.12 r_work: 0.3628 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8513 Z= 0.206 Angle : 0.675 15.486 11551 Z= 0.353 Chirality : 0.047 0.156 1287 Planarity : 0.005 0.064 1465 Dihedral : 7.650 154.309 1152 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.65 % Allowed : 11.16 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 (0.25), residues: 1031 helix: 1.04 (0.26), residues: 388 sheet: 0.11 (0.32), residues: 233 loop : -0.94 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.032 0.002 TYR B 59 PHE 0.021 0.002 PHE R 190 TRP 0.023 0.002 TRP B 339 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 ( 8509) covalent geometry : angle 0.67246 / 0.35 (11543) SS BOND : bond 0.00299 / 0.15 ( 4) SS BOND : angle 2.22785 / 0.92 ( 8) hydrogen bonds : bond 0.05556 / 3.78 ( 409) hydrogen bonds : angle 4.88684 / 3.40 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.227 Fit side-chains REVERT: B 59 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: B 219 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7243 (mmm-85) REVERT: N 73 ASP cc_start: 0.8061 (m-30) cc_final: 0.7757 (m-30) REVERT: N 80 TYR cc_start: 0.8649 (m-80) cc_final: 0.8435 (m-80) REVERT: R 137 VAL cc_start: 0.8751 (p) cc_final: 0.7872 (m) REVERT: R 212 TYR cc_start: 0.7202 (m-80) cc_final: 0.6936 (m-10) REVERT: R 235 LYS cc_start: 0.7564 (tppp) cc_final: 0.7282 (tptp) REVERT: R 265 MET cc_start: 0.5408 (tmm) cc_final: 0.4082 (mtt) REVERT: A 25 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8123 (ttmp) REVERT: A 35 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: A 61 ARG cc_start: 0.6905 (mtt180) cc_final: 0.6572 (mtt180) REVERT: A 253 TYR cc_start: 0.8580 (m-80) cc_final: 0.8310 (m-80) REVERT: A 343 ASP cc_start: 0.8424 (m-30) cc_final: 0.8109 (m-30) REVERT: A 370 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7455 (mp0) outliers start: 24 outliers final: 11 residues processed: 213 average time/residue: 0.4628 time to fit residues: 104.9349 Evaluate side-chains 194 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 87 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 77 ASN R 151 GLN A 14 ASN A 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151163 restraints weight = 9401.507| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.09 r_work: 0.3658 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8513 Z= 0.142 Angle : 0.604 14.672 11551 Z= 0.312 Chirality : 0.044 0.164 1287 Planarity : 0.004 0.052 1465 Dihedral : 7.444 157.087 1152 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 13.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.27 (0.25), residues: 1031 helix: 1.42 (0.26), residues: 388 sheet: 0.10 (0.31), residues: 231 loop : -0.94 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.021 0.002 TYR B 59 PHE 0.018 0.002 PHE A 212 TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8509) covalent geometry : angle 0.60290 / 0.31 (11543) SS BOND : bond 0.00281 / 0.14 ( 4) SS BOND : angle 1.53311 / 0.69 ( 8) hydrogen bonds : bond 0.04877 / 3.30 ( 409) hydrogen bonds : angle 4.62429 / 3.21 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: B 219 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: N 73 ASP cc_start: 0.8040 (m-30) cc_final: 0.7706 (m-30) REVERT: N 80 TYR cc_start: 0.8633 (m-80) cc_final: 0.8350 (m-80) REVERT: R 137 VAL cc_start: 0.8741 (p) cc_final: 0.7857 (m) REVERT: R 143 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8222 (tp) REVERT: R 198 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7765 (mm) REVERT: R 235 LYS cc_start: 0.7653 (tppp) cc_final: 0.7328 (tptp) REVERT: R 265 MET cc_start: 0.5453 (tmm) cc_final: 0.4097 (mtt) REVERT: A 25 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8125 (ttmp) REVERT: A 35 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: A 253 TYR cc_start: 0.8611 (m-80) cc_final: 0.8410 (m-80) REVERT: A 370 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7471 (mp0) outliers start: 30 outliers final: 15 residues processed: 205 average time/residue: 0.5238 time to fit residues: 114.4751 Evaluate side-chains 200 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 115 GLN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 0.0030 chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 77 ASN R 151 GLN A 14 ASN A 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.191820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151478 restraints weight = 9553.722| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.10 r_work: 0.3665 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8513 Z= 0.135 Angle : 0.579 13.370 11551 Z= 0.302 Chirality : 0.044 0.157 1287 Planarity : 0.004 0.051 1465 Dihedral : 7.307 156.375 1152 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 15.25 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1031 helix: 1.56 (0.26), residues: 388 sheet: 0.04 (0.31), residues: 231 loop : -0.95 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.023 0.002 TYR R 284 PHE 0.019 0.001 PHE A 212 TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8509) covalent geometry : angle 0.57567 / 0.30 (11543) SS BOND : bond 0.00150 / 0.07 ( 4) SS BOND : angle 2.54260 / 1.10 ( 8) hydrogen bonds : bond 0.04638 / 3.13 ( 409) hydrogen bonds : angle 4.52729 / 3.15 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: B 219 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7346 (mmm-85) REVERT: N 73 ASP cc_start: 0.8015 (m-30) cc_final: 0.7733 (m-30) REVERT: N 80 TYR cc_start: 0.8615 (m-80) cc_final: 0.8376 (m-80) REVERT: R 137 VAL cc_start: 0.8744 (p) cc_final: 0.7867 (m) REVERT: R 143 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8168 (tp) REVERT: R 190 PHE cc_start: 0.8111 (m-80) cc_final: 0.7762 (m-80) REVERT: R 235 LYS cc_start: 0.7620 (tppp) cc_final: 0.7309 (tptp) REVERT: R 265 MET cc_start: 0.5467 (tmm) cc_final: 0.4073 (mtt) REVERT: R 284 TYR cc_start: 0.8297 (t80) cc_final: 0.8010 (t80) REVERT: A 25 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8090 (ttmp) REVERT: A 35 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: A 296 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8347 (mt) REVERT: A 370 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7504 (mp0) outliers start: 33 outliers final: 19 residues processed: 205 average time/residue: 0.5339 time to fit residues: 116.6387 Evaluate side-chains 203 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 0.0370 chunk 51 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 77 ASN R 151 GLN A 14 ASN A 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.192712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152586 restraints weight = 9518.461| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.10 r_work: 0.3676 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8513 Z= 0.127 Angle : 0.580 13.317 11551 Z= 0.301 Chirality : 0.043 0.174 1287 Planarity : 0.004 0.052 1465 Dihedral : 7.220 156.186 1152 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.09 % Allowed : 16.02 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.26), residues: 1031 helix: 1.52 (0.26), residues: 390 sheet: 0.10 (0.31), residues: 233 loop : -0.88 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.020 0.001 TYR R 284 PHE 0.018 0.001 PHE A 212 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8509) covalent geometry : angle 0.57133 / 0.30 (11543) SS BOND : bond 0.00239 / 0.12 ( 4) SS BOND : angle 3.80022 / 1.48 ( 8) hydrogen bonds : bond 0.04466 / 3.03 ( 409) hydrogen bonds : angle 4.47944 / 3.13 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: B 197 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6619 (mtm110) REVERT: B 219 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7378 (mmm-85) REVERT: B 262 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8337 (mpt) REVERT: N 73 ASP cc_start: 0.8023 (m-30) cc_final: 0.7758 (m-30) REVERT: N 80 TYR cc_start: 0.8584 (m-80) cc_final: 0.8348 (m-80) REVERT: R 137 VAL cc_start: 0.8728 (p) cc_final: 0.8502 (t) REVERT: R 143 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8165 (tp) REVERT: R 243 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7699 (ttt180) REVERT: R 265 MET cc_start: 0.5463 (tmm) cc_final: 0.4077 (mtt) REVERT: R 284 TYR cc_start: 0.8313 (t80) cc_final: 0.8019 (t80) REVERT: A 17 LYS cc_start: 0.8437 (pttm) cc_final: 0.8155 (pttm) REVERT: A 25 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8082 (ttmp) REVERT: A 35 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: A 59 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5592 (mp10) REVERT: A 296 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 370 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7537 (mp0) outliers start: 37 outliers final: 17 residues processed: 214 average time/residue: 0.4834 time to fit residues: 110.5636 Evaluate side-chains 207 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN R 151 GLN A 14 ASN A 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.190392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149822 restraints weight = 9414.111| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.13 r_work: 0.3646 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8513 Z= 0.169 Angle : 0.621 14.922 11551 Z= 0.324 Chirality : 0.045 0.173 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.362 155.956 1152 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.76 % Allowed : 18.01 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.32 (0.26), residues: 1031 helix: 1.43 (0.26), residues: 391 sheet: 0.03 (0.31), residues: 239 loop : -0.83 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.026 0.002 TYR B 59 PHE 0.020 0.002 PHE A 212 TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 8509) covalent geometry : angle 0.61223 / 0.32 (11543) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 3.90496 / 1.55 ( 8) hydrogen bonds : bond 0.04887 / 3.32 ( 409) hydrogen bonds : angle 4.63670 / 3.24 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: B 197 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6589 (mtm110) REVERT: B 219 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7213 (mmm-85) REVERT: N 73 ASP cc_start: 0.8056 (m-30) cc_final: 0.7798 (m-30) REVERT: N 77 ASN cc_start: 0.8319 (m-40) cc_final: 0.8100 (m110) REVERT: N 80 TYR cc_start: 0.8641 (m-80) cc_final: 0.8423 (m-80) REVERT: R 137 VAL cc_start: 0.8731 (p) cc_final: 0.8526 (t) REVERT: R 143 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8175 (tp) REVERT: R 212 TYR cc_start: 0.7260 (m-80) cc_final: 0.6917 (m-80) REVERT: R 235 LYS cc_start: 0.7645 (tppp) cc_final: 0.7363 (tppp) REVERT: R 265 MET cc_start: 0.5360 (tmm) cc_final: 0.4003 (mtt) REVERT: R 284 TYR cc_start: 0.8308 (t80) cc_final: 0.8015 (t80) REVERT: A 16 GLU cc_start: 0.7639 (tp30) cc_final: 0.7253 (tm-30) REVERT: A 25 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8045 (ttmp) REVERT: A 35 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: A 296 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8265 (mt) REVERT: A 370 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7443 (mp0) outliers start: 34 outliers final: 19 residues processed: 210 average time/residue: 0.5391 time to fit residues: 120.4300 Evaluate side-chains 210 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN R 151 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150845 restraints weight = 9537.250| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.11 r_work: 0.3652 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8513 Z= 0.152 Angle : 0.617 14.431 11551 Z= 0.321 Chirality : 0.044 0.193 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.311 156.024 1152 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 18.01 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1031 helix: 1.42 (0.27), residues: 391 sheet: -0.01 (0.31), residues: 239 loop : -0.83 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.023 0.002 TYR B 59 PHE 0.019 0.001 PHE A 212 TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8509) covalent geometry : angle 0.61168 / 0.32 (11543) SS BOND : bond 0.00167 / 0.08 ( 4) SS BOND : angle 3.16617 / 1.28 ( 8) hydrogen bonds : bond 0.04715 / 3.21 ( 409) hydrogen bonds : angle 4.63639 / 3.23 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7596 (m-10) REVERT: B 219 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7363 (mmm-85) REVERT: N 73 ASP cc_start: 0.8063 (m-30) cc_final: 0.7794 (m-30) REVERT: N 80 TYR cc_start: 0.8628 (m-80) cc_final: 0.8382 (m-80) REVERT: R 137 VAL cc_start: 0.8740 (p) cc_final: 0.8533 (t) REVERT: R 143 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8239 (tp) REVERT: R 212 TYR cc_start: 0.7276 (m-80) cc_final: 0.6996 (m-80) REVERT: R 235 LYS cc_start: 0.7647 (tppp) cc_final: 0.7367 (tppp) REVERT: R 265 MET cc_start: 0.5392 (tmm) cc_final: 0.4042 (mtt) REVERT: R 284 TYR cc_start: 0.8291 (t80) cc_final: 0.7996 (t80) REVERT: A 16 GLU cc_start: 0.7696 (tp30) cc_final: 0.7327 (tm-30) REVERT: A 25 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8111 (ttmp) REVERT: A 35 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: A 296 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 370 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7508 (mp0) outliers start: 36 outliers final: 20 residues processed: 211 average time/residue: 0.5052 time to fit residues: 113.7995 Evaluate side-chains 209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 77 ASN N 120 GLN R 151 GLN A 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.192201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151647 restraints weight = 9485.782| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.14 r_work: 0.3668 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8513 Z= 0.141 Angle : 0.611 14.240 11551 Z= 0.318 Chirality : 0.044 0.200 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.266 155.753 1152 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.43 % Allowed : 18.90 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1031 helix: 1.43 (0.27), residues: 391 sheet: -0.00 (0.31), residues: 239 loop : -0.82 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.022 0.002 TYR B 59 PHE 0.019 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8509) covalent geometry : angle 0.60588 / 0.32 (11543) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 3.12516 / 1.26 ( 8) hydrogen bonds : bond 0.04610 / 3.13 ( 409) hydrogen bonds : angle 4.60611 / 3.21 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: B 219 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7275 (mmm-85) REVERT: N 73 ASP cc_start: 0.8033 (m-30) cc_final: 0.7735 (m-30) REVERT: N 80 TYR cc_start: 0.8602 (m-80) cc_final: 0.8341 (m-80) REVERT: R 71 LEU cc_start: 0.3127 (OUTLIER) cc_final: 0.2898 (pt) REVERT: R 137 VAL cc_start: 0.8669 (p) cc_final: 0.8460 (t) REVERT: R 143 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8178 (tp) REVERT: R 212 TYR cc_start: 0.7232 (m-80) cc_final: 0.6959 (m-80) REVERT: R 235 LYS cc_start: 0.7630 (tppp) cc_final: 0.7167 (tppp) REVERT: R 265 MET cc_start: 0.5331 (tmm) cc_final: 0.3969 (mtt) REVERT: R 284 TYR cc_start: 0.8275 (t80) cc_final: 0.7967 (t80) REVERT: A 16 GLU cc_start: 0.7666 (tp30) cc_final: 0.7270 (tm-30) REVERT: A 25 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8053 (ttmp) REVERT: A 35 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8199 (mp10) REVERT: A 296 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 370 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7451 (mp0) outliers start: 31 outliers final: 20 residues processed: 203 average time/residue: 0.5328 time to fit residues: 115.3981 Evaluate side-chains 209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain R residue 115 GLN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 31 ASN N 120 GLN R 151 GLN A 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.190850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150186 restraints weight = 9481.125| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.15 r_work: 0.3650 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8513 Z= 0.166 Angle : 0.638 14.980 11551 Z= 0.331 Chirality : 0.045 0.207 1287 Planarity : 0.005 0.059 1465 Dihedral : 7.331 155.677 1152 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.54 % Allowed : 19.45 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.27 (0.26), residues: 1031 helix: 1.36 (0.27), residues: 391 sheet: -0.01 (0.31), residues: 239 loop : -0.83 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 265 TYR 0.025 0.002 TYR B 59 PHE 0.019 0.002 PHE A 212 TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8509) covalent geometry : angle 0.63321 / 0.33 (11543) SS BOND : bond 0.00179 / 0.09 ( 4) SS BOND : angle 2.96770 / 1.22 ( 8) hydrogen bonds : bond 0.04849 / 3.30 ( 409) hydrogen bonds : angle 4.70708 / 3.29 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7639 (m-10) REVERT: B 219 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7263 (mmm-85) REVERT: N 5 GLN cc_start: 0.6586 (mm-40) cc_final: 0.6370 (mm-40) REVERT: N 73 ASP cc_start: 0.8056 (m-30) cc_final: 0.7758 (m-30) REVERT: N 80 TYR cc_start: 0.8644 (m-80) cc_final: 0.8380 (m-80) REVERT: R 138 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.8027 (t70) REVERT: R 143 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8188 (tp) REVERT: R 212 TYR cc_start: 0.7259 (m-80) cc_final: 0.6984 (m-80) REVERT: R 235 LYS cc_start: 0.7625 (tppp) cc_final: 0.7148 (tppp) REVERT: R 265 MET cc_start: 0.5337 (tmm) cc_final: 0.3992 (mtt) REVERT: R 284 TYR cc_start: 0.8258 (t80) cc_final: 0.7934 (t80) REVERT: A 16 GLU cc_start: 0.7683 (tp30) cc_final: 0.7296 (tm-30) REVERT: A 25 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (ttmp) REVERT: A 35 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: A 307 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8027 (mmtm) REVERT: A 370 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7444 (mp0) outliers start: 32 outliers final: 19 residues processed: 206 average time/residue: 0.5530 time to fit residues: 121.0011 Evaluate side-chains 204 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 0.0270 chunk 7 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 77 ASN N 120 GLN R 151 GLN A 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.193514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152759 restraints weight = 9411.567| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.12 r_work: 0.3659 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8513 Z= 0.137 Angle : 0.630 13.922 11551 Z= 0.324 Chirality : 0.044 0.208 1287 Planarity : 0.004 0.065 1465 Dihedral : 7.231 155.000 1152 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.09 % Allowed : 20.00 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1031 helix: 1.43 (0.27), residues: 391 sheet: 0.05 (0.31), residues: 237 loop : -0.82 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 265 TYR 0.022 0.002 TYR B 59 PHE 0.018 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8509) covalent geometry : angle 0.62639 / 0.32 (11543) SS BOND : bond 0.00131 / 0.06 ( 4) SS BOND : angle 2.63663 / 1.09 ( 8) hydrogen bonds : bond 0.04599 / 3.13 ( 409) hydrogen bonds : angle 4.64665 / 3.24 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: B 75 GLN cc_start: 0.8443 (mt0) cc_final: 0.8237 (mt0) REVERT: B 219 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7256 (mmm-85) REVERT: N 73 ASP cc_start: 0.8046 (m-30) cc_final: 0.7773 (m-30) REVERT: N 80 TYR cc_start: 0.8617 (m-80) cc_final: 0.8386 (m-80) REVERT: R 115 GLN cc_start: 0.8555 (mp10) cc_final: 0.7910 (mp10) REVERT: R 143 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (tp) REVERT: R 212 TYR cc_start: 0.7191 (m-80) cc_final: 0.6910 (m-80) REVERT: R 235 LYS cc_start: 0.7611 (tppp) cc_final: 0.7286 (tptp) REVERT: R 265 MET cc_start: 0.5330 (tmm) cc_final: 0.3955 (mtt) REVERT: R 284 TYR cc_start: 0.8228 (t80) cc_final: 0.7897 (t80) REVERT: A 16 GLU cc_start: 0.7724 (tp30) cc_final: 0.7279 (tm-30) REVERT: A 25 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8033 (ttmp) REVERT: A 35 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: A 370 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7419 (mp0) outliers start: 28 outliers final: 17 residues processed: 199 average time/residue: 0.5351 time to fit residues: 113.7264 Evaluate side-chains 198 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 chunk 85 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN N 120 GLN R 151 GLN A 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.193910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153685 restraints weight = 9418.914| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.13 r_work: 0.3670 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8513 Z= 0.138 Angle : 0.633 14.107 11551 Z= 0.325 Chirality : 0.044 0.207 1287 Planarity : 0.004 0.054 1465 Dihedral : 7.223 155.339 1152 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.98 % Allowed : 20.44 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.26), residues: 1031 helix: 1.46 (0.27), residues: 391 sheet: 0.06 (0.31), residues: 237 loop : -0.80 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 265 TYR 0.022 0.002 TYR B 59 PHE 0.018 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8509) covalent geometry : angle 0.63024 / 0.32 (11543) SS BOND : bond 0.00151 / 0.07 ( 4) SS BOND : angle 2.45712 / 1.04 ( 8) hydrogen bonds : bond 0.04605 / 3.13 ( 409) hydrogen bonds : angle 4.61994 / 3.23 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.09 seconds wall clock time: 66 minutes 59.97 seconds (4019.97 seconds total)