Starting phenix.real_space_refine on Tue Mar 3 19:53:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmp_34902/03_2026/8hmp_34902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmp_34902/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hmp_34902/03_2026/8hmp_34902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmp_34902/03_2026/8hmp_34902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmp_34902/03_2026/8hmp_34902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmp_34902/03_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-5986/lib/python3.9/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: 0.57 Conformation dependent library (CDL) restraints added in 313.3 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: 0.26 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: 1.16 Time building geometry restraints manager: 0.76 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: 4833 27.41 - 54.82: 164 54.82 - 82.23: 26 82.23 - 109.64: 1 109.64 - 137.04: 1 Dihedral angle restraints: 5025 sinusoidal: 1979 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 5022 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: 6.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 14.082 137.044 3047 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 covalent geometry : bond 0.00517 ( 8509) covalent geometry : angle 0.91867 (11543) SS BOND : bond 0.00557 ( 4) SS BOND : angle 1.59977 ( 8) hydrogen bonds : bond 0.13521 ( 409) hydrogen bonds : angle 5.99898 ( 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 : 0.293 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: 0.5504 time to fit residues: 141.6219 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 : 0.293 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4190 r_free = 0.4190 target = 0.189805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148791 restraints weight = 9520.868| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.13 r_work: 0.3626 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1547 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 15.527 11551 Z= 0.354 Chirality : 0.047 0.156 1287 Planarity : 0.005 0.064 1465 Dihedral : 7.621 153.300 1156 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.54 % Allowed : 11.27 % 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: 0.05 (0.25), residues: 1031 helix: 1.05 (0.26), residues: 388 sheet: 0.12 (0.32), residues: 232 loop : -0.95 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.031 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 covalent geometry : bond 0.00460 ( 8509) covalent geometry : angle 0.67337 (11543) SS BOND : bond 0.00309 ( 4) SS BOND : angle 2.10851 ( 8) hydrogen bonds : bond 0.05514 ( 409) hydrogen bonds : angle 4.88192 ( 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 229 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.388 Fit side-chains REVERT: B 59 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7805 (m-10) REVERT: B 219 ARG cc_start: 0.7767 (mmm-85) cc_final: 0.7252 (mmm-85) REVERT: N 73 ASP cc_start: 0.8062 (m-30) cc_final: 0.7755 (m-30) REVERT: N 80 TYR cc_start: 0.8649 (m-80) cc_final: 0.8440 (m-80) REVERT: R 137 VAL cc_start: 0.8753 (p) cc_final: 0.7874 (m) REVERT: R 212 TYR cc_start: 0.7195 (m-80) cc_final: 0.6928 (m-10) REVERT: R 235 LYS cc_start: 0.7566 (tppp) cc_final: 0.7288 (tptp) REVERT: R 265 MET cc_start: 0.5426 (tmm) cc_final: 0.4096 (mtt) REVERT: A 25 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8118 (ttmp) REVERT: A 35 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: A 61 ARG cc_start: 0.6868 (mtt180) cc_final: 0.6523 (mtt180) REVERT: A 253 TYR cc_start: 0.8581 (m-80) cc_final: 0.8309 (m-80) REVERT: A 343 ASP cc_start: 0.8444 (m-30) cc_final: 0.8168 (m-30) REVERT: A 370 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7455 (mp0) outliers start: 23 outliers final: 11 residues processed: 212 average time/residue: 0.5531 time to fit residues: 124.2756 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 : 0.272 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.0270 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4218 r_free = 0.4218 target = 0.192687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152212 restraints weight = 9392.581| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.11 r_work: 0.3677 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8513 Z= 0.124 Angle : 0.586 13.955 11551 Z= 0.302 Chirality : 0.044 0.163 1287 Planarity : 0.004 0.051 1465 Dihedral : 7.358 156.858 1156 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.09 % Allowed : 13.81 % Favored : 83.09 % 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 (0.25), residues: 1031 helix: 1.48 (0.26), residues: 388 sheet: 0.15 (0.31), residues: 230 loop : -0.96 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.019 0.001 TYR B 59 PHE 0.018 0.001 PHE A 212 TRP 0.015 0.002 TRP B 339 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8509) covalent geometry : angle 0.58440 (11543) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.49264 ( 8) hydrogen bonds : bond 0.04658 ( 409) hydrogen bonds : angle 4.55048 ( 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 223 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7303 (m-10) REVERT: B 219 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7074 (mmm-85) REVERT: N 73 ASP cc_start: 0.8040 (m-30) cc_final: 0.7706 (m-30) REVERT: N 80 TYR cc_start: 0.8610 (m-80) cc_final: 0.8341 (m-80) REVERT: R 137 VAL cc_start: 0.8672 (p) cc_final: 0.7799 (m) REVERT: R 143 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8178 (tp) REVERT: R 198 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7682 (mm) REVERT: R 235 LYS cc_start: 0.7639 (tppp) cc_final: 0.7298 (tptp) REVERT: R 265 MET cc_start: 0.5387 (tmm) cc_final: 0.4017 (mtt) REVERT: A 25 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8049 (ttmp) REVERT: A 35 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: A 253 TYR cc_start: 0.8577 (m-80) cc_final: 0.8324 (m-80) REVERT: A 296 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8388 (mt) REVERT: A 370 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7453 (mp0) outliers start: 28 outliers final: 12 residues processed: 210 average time/residue: 0.5363 time to fit residues: 119.5907 Evaluate side-chains 201 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 G residue 22 GLU Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 115 GLN Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU 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 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 296 LEU Chi-restraints excluded: chain A residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 0.0070 chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4221 r_free = 0.4221 target = 0.192938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152677 restraints weight = 9548.671| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.09 r_work: 0.3680 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8513 Z= 0.123 Angle : 0.561 12.515 11551 Z= 0.293 Chirality : 0.043 0.155 1287 Planarity : 0.004 0.051 1465 Dihedral : 7.226 156.422 1156 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.31 % Allowed : 15.36 % Favored : 81.33 % 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: 0.40 (0.25), residues: 1031 helix: 1.62 (0.26), residues: 389 sheet: 0.11 (0.31), residues: 230 loop : -0.93 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.022 0.001 TYR R 284 PHE 0.019 0.001 PHE A 212 TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8509) covalent geometry : angle 0.55674 (11543) SS BOND : bond 0.00271 ( 4) SS BOND : angle 2.59362 ( 8) hydrogen bonds : bond 0.04456 ( 409) hydrogen bonds : angle 4.45500 ( 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 230 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: B 219 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7305 (mmm-85) REVERT: N 73 ASP cc_start: 0.8043 (m-30) cc_final: 0.7754 (m-30) REVERT: N 80 TYR cc_start: 0.8598 (m-80) cc_final: 0.8318 (m-80) REVERT: R 137 VAL cc_start: 0.8708 (p) cc_final: 0.8479 (t) REVERT: R 143 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (tp) REVERT: R 190 PHE cc_start: 0.8109 (m-80) cc_final: 0.7730 (m-80) REVERT: R 198 LEU cc_start: 0.8216 (mt) cc_final: 0.7735 (mm) REVERT: R 235 LYS cc_start: 0.7621 (tppp) cc_final: 0.7314 (tptp) REVERT: R 265 MET cc_start: 0.5492 (tmm) cc_final: 0.4054 (mtt) REVERT: R 284 TYR cc_start: 0.8276 (t80) cc_final: 0.7986 (t80) REVERT: A 25 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8062 (ttmp) REVERT: A 35 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: A 370 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7517 (mp0) outliers start: 30 outliers final: 15 residues processed: 215 average time/residue: 0.5255 time to fit residues: 120.5887 Evaluate side-chains 203 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 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 369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4196 r_free = 0.4196 target = 0.190559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150144 restraints weight = 9539.620| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.12 r_work: 0.3642 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8513 Z= 0.170 Angle : 0.618 14.574 11551 Z= 0.321 Chirality : 0.045 0.182 1287 Planarity : 0.004 0.052 1465 Dihedral : 7.340 156.439 1156 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.87 % Allowed : 16.57 % Favored : 79.56 % 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: 0.29 (0.26), residues: 1031 helix: 1.44 (0.26), residues: 389 sheet: 0.05 (0.31), residues: 231 loop : -0.89 (0.30), residues: 411 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 0.015 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8509) covalent geometry : angle 0.61024 (11543) SS BOND : bond 0.00138 ( 4) SS BOND : angle 3.79587 ( 8) hydrogen bonds : bond 0.04880 ( 409) hydrogen bonds : angle 4.60476 ( 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 222 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: B 197 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6619 (mtm110) REVERT: B 219 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7318 (mmm-85) REVERT: N 73 ASP cc_start: 0.8065 (m-30) cc_final: 0.7807 (m-30) REVERT: N 80 TYR cc_start: 0.8645 (m-80) cc_final: 0.8430 (m-80) REVERT: R 137 VAL cc_start: 0.8761 (p) cc_final: 0.8561 (t) REVERT: R 143 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8210 (tp) REVERT: R 212 TYR cc_start: 0.7238 (m-80) cc_final: 0.6927 (m-80) REVERT: R 265 MET cc_start: 0.5441 (tmm) cc_final: 0.4084 (mtt) REVERT: R 284 TYR cc_start: 0.8318 (t80) cc_final: 0.8017 (t80) REVERT: A 35 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: A 59 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.5771 (mp10) REVERT: A 296 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8311 (mt) REVERT: A 370 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7506 (mp0) outliers start: 35 outliers final: 20 residues processed: 205 average time/residue: 0.5355 time to fit residues: 116.5792 Evaluate side-chains 206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 R residue 286 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 15 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 18 GLN 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 = 0.4214 r_free = 0.4214 target = 0.192088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151995 restraints weight = 9405.601| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.08 r_work: 0.3673 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8513 Z= 0.133 Angle : 0.595 13.432 11551 Z= 0.308 Chirality : 0.044 0.183 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.232 155.740 1156 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.87 % Allowed : 17.68 % Favored : 78.45 % 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: 0.36 (0.26), residues: 1031 helix: 1.47 (0.26), residues: 391 sheet: 0.02 (0.31), residues: 239 loop : -0.81 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.021 0.001 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 covalent geometry : bond 0.00294 ( 8509) covalent geometry : angle 0.58788 (11543) SS BOND : bond 0.00175 ( 4) SS BOND : angle 3.54519 ( 8) hydrogen bonds : bond 0.04522 ( 409) hydrogen bonds : angle 4.53835 ( 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 227 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7477 (m-10) REVERT: B 219 ARG cc_start: 0.7679 (mmm-85) cc_final: 0.7284 (mmm-85) REVERT: B 262 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8310 (mpt) REVERT: G 18 GLN cc_start: 0.4387 (OUTLIER) cc_final: 0.4044 (tp-100) REVERT: N 73 ASP cc_start: 0.8006 (m-30) cc_final: 0.7729 (m-30) REVERT: N 77 ASN cc_start: 0.8318 (m-40) cc_final: 0.8117 (m110) REVERT: N 80 TYR cc_start: 0.8598 (m-80) cc_final: 0.8335 (m-80) REVERT: R 137 VAL cc_start: 0.8741 (p) cc_final: 0.8541 (t) REVERT: R 143 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8134 (tp) REVERT: R 212 TYR cc_start: 0.7176 (m-80) cc_final: 0.6891 (m-80) REVERT: R 235 LYS cc_start: 0.7668 (tppp) cc_final: 0.7401 (tppp) REVERT: R 265 MET cc_start: 0.5472 (tmm) cc_final: 0.4097 (mtt) REVERT: R 284 TYR cc_start: 0.8287 (t80) cc_final: 0.7980 (t80) REVERT: A 35 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: A 59 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5487 (mp10) REVERT: A 296 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 370 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7503 (mp0) outliers start: 35 outliers final: 19 residues processed: 215 average time/residue: 0.5321 time to fit residues: 121.5593 Evaluate side-chains 214 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 18 GLN 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 A residue 9 THR 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 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: 0.5980 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 18 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 = 0.4199 r_free = 0.4199 target = 0.190840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150752 restraints weight = 9580.672| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.11 r_work: 0.3648 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8513 Z= 0.167 Angle : 0.626 14.592 11551 Z= 0.325 Chirality : 0.045 0.194 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.307 156.388 1156 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.09 % Allowed : 17.90 % 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: 0.32 (0.26), residues: 1031 helix: 1.42 (0.26), residues: 391 sheet: 0.02 (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 0.024 0.002 TYR B 59 PHE 0.020 0.002 PHE A 212 TRP 0.013 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8509) covalent geometry : angle 0.62056 (11543) SS BOND : bond 0.00180 ( 4) SS BOND : angle 3.15120 ( 8) hydrogen bonds : bond 0.04791 ( 409) hydrogen bonds : angle 4.64269 ( 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 229 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: B 214 ARG cc_start: 0.8006 (mpp-170) cc_final: 0.7759 (mpp-170) REVERT: B 219 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7261 (mmm-85) REVERT: N 73 ASP cc_start: 0.8060 (m-30) cc_final: 0.7815 (m-30) REVERT: N 80 TYR cc_start: 0.8642 (m-80) cc_final: 0.8430 (m-80) REVERT: R 71 LEU cc_start: 0.3046 (OUTLIER) cc_final: 0.2807 (pt) REVERT: R 143 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8199 (tp) REVERT: R 212 TYR cc_start: 0.7279 (m-80) cc_final: 0.6999 (m-80) REVERT: R 235 LYS cc_start: 0.7642 (tppp) cc_final: 0.7224 (tppp) REVERT: R 265 MET cc_start: 0.5424 (tmm) cc_final: 0.4065 (mtt) REVERT: R 284 TYR cc_start: 0.8293 (t80) cc_final: 0.7986 (t80) REVERT: A 35 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: A 59 GLN cc_start: 0.5817 (OUTLIER) cc_final: 0.5414 (mp10) REVERT: A 296 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8338 (mt) REVERT: A 370 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7504 (mp0) outliers start: 37 outliers final: 21 residues processed: 214 average time/residue: 0.5197 time to fit residues: 118.1255 Evaluate side-chains 213 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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 15 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 77 ASN 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 = 0.4209 r_free = 0.4209 target = 0.191556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151462 restraints weight = 9470.164| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.09 r_work: 0.3648 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8513 Z= 0.151 Angle : 0.635 14.340 11551 Z= 0.328 Chirality : 0.044 0.201 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.292 156.068 1156 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 19.01 % Favored : 77.79 % 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: 1.41 (0.26), residues: 390 sheet: 0.01 (0.31), residues: 239 loop : -0.83 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.024 0.002 TYR B 59 PHE 0.019 0.002 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8509) covalent geometry : angle 0.62960 (11543) SS BOND : bond 0.00321 ( 4) SS BOND : angle 3.27313 ( 8) hydrogen bonds : bond 0.04709 ( 409) hydrogen bonds : angle 4.64639 ( 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 216 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: B 219 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7294 (mmm-85) REVERT: N 73 ASP cc_start: 0.8052 (m-30) cc_final: 0.7779 (m-30) REVERT: N 80 TYR cc_start: 0.8625 (m-80) cc_final: 0.8384 (m-80) REVERT: R 212 TYR cc_start: 0.7267 (m-80) cc_final: 0.6995 (m-80) REVERT: R 235 LYS cc_start: 0.7635 (tppp) cc_final: 0.7212 (tppp) REVERT: R 243 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7671 (ttt180) REVERT: R 265 MET cc_start: 0.5374 (tmm) cc_final: 0.4029 (mtt) REVERT: R 284 TYR cc_start: 0.8251 (t80) cc_final: 0.7945 (t80) REVERT: A 16 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 20 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7111 (mtp85) REVERT: A 35 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: A 59 GLN cc_start: 0.5736 (OUTLIER) cc_final: 0.5397 (mp10) REVERT: A 296 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 342 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.8180 (ttt-90) REVERT: A 370 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7487 (mp0) outliers start: 29 outliers final: 21 residues processed: 206 average time/residue: 0.5338 time to fit residues: 116.9834 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 : 0.230 ------------------------------------------------------------------------------- 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 115 GLN Chi-restraints excluded: chain R residue 132 LEU 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 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 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: 0.9980 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN 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 = 0.4202 r_free = 0.4202 target = 0.190971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150423 restraints weight = 9491.356| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.14 r_work: 0.3652 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8513 Z= 0.162 Angle : 0.649 14.804 11551 Z= 0.335 Chirality : 0.045 0.209 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.325 155.673 1156 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.65 % Allowed : 19.34 % 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: 0.26 (0.26), residues: 1031 helix: 1.35 (0.27), residues: 390 sheet: -0.01 (0.31), residues: 239 loop : -0.83 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.024 0.002 TYR B 59 PHE 0.019 0.002 PHE A 212 TRP 0.013 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8509) covalent geometry : angle 0.64403 (11543) SS BOND : bond 0.00259 ( 4) SS BOND : angle 3.03219 ( 8) hydrogen bonds : bond 0.04824 ( 409) hydrogen bonds : angle 4.71040 ( 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 222 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7715 (m-10) REVERT: B 219 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7226 (mmm-85) REVERT: N 73 ASP cc_start: 0.8055 (m-30) cc_final: 0.7759 (m-30) REVERT: N 77 ASN cc_start: 0.8292 (m-40) cc_final: 0.8068 (m110) REVERT: N 80 TYR cc_start: 0.8650 (m-80) cc_final: 0.8389 (m-80) REVERT: R 212 TYR cc_start: 0.7246 (m-80) cc_final: 0.6979 (m-80) REVERT: R 235 LYS cc_start: 0.7619 (tppp) cc_final: 0.7175 (tppp) REVERT: R 265 MET cc_start: 0.5335 (tmm) cc_final: 0.3997 (mtt) REVERT: R 284 TYR cc_start: 0.8256 (t80) cc_final: 0.7933 (t80) REVERT: R 285 PHE cc_start: 0.8291 (t80) cc_final: 0.8032 (t80) REVERT: R 286 LEU cc_start: 0.8882 (mm) cc_final: 0.8657 (mm) REVERT: A 16 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 20 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7101 (mtp85) REVERT: A 35 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: A 59 GLN cc_start: 0.5633 (OUTLIER) cc_final: 0.5307 (mp10) REVERT: A 370 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7412 (mp0) outliers start: 33 outliers final: 19 residues processed: 210 average time/residue: 0.5657 time to fit residues: 126.0417 Evaluate side-chains 205 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 62 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4237 r_free = 0.4237 target = 0.194741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.154831 restraints weight = 9458.871| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.08 r_work: 0.3700 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8513 Z= 0.119 Angle : 0.612 12.811 11551 Z= 0.315 Chirality : 0.043 0.201 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.123 155.086 1156 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.76 % Allowed : 20.55 % Favored : 76.69 % 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: 0.42 (0.26), residues: 1031 helix: 1.52 (0.27), residues: 390 sheet: 0.11 (0.31), residues: 236 loop : -0.80 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.023 0.001 TYR R 284 PHE 0.018 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8509) covalent geometry : angle 0.60900 (11543) SS BOND : bond 0.00098 ( 4) SS BOND : angle 2.47394 ( 8) hydrogen bonds : bond 0.04314 ( 409) hydrogen bonds : angle 4.54963 ( 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 217 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: B 219 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7290 (mmm-85) REVERT: N 73 ASP cc_start: 0.8028 (m-30) cc_final: 0.7803 (m-30) REVERT: N 77 ASN cc_start: 0.8231 (m-40) cc_final: 0.8011 (m110) REVERT: R 115 GLN cc_start: 0.8562 (mp10) cc_final: 0.8006 (mp10) REVERT: R 235 LYS cc_start: 0.7611 (tppp) cc_final: 0.7279 (tptp) REVERT: R 265 MET cc_start: 0.5397 (tmm) cc_final: 0.4001 (mtt) REVERT: R 284 TYR cc_start: 0.8225 (t80) cc_final: 0.7895 (t80) REVERT: A 35 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: A 59 GLN cc_start: 0.5597 (OUTLIER) cc_final: 0.5332 (mp10) REVERT: A 307 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (mmtm) REVERT: A 370 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7475 (mp0) outliers start: 25 outliers final: 16 residues processed: 209 average time/residue: 0.5224 time to fit residues: 116.4900 Evaluate side-chains 208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 158 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain A residue 9 THR 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 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 97 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4205 r_free = 0.4205 target = 0.191636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151442 restraints weight = 9489.143| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.11 r_work: 0.3654 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8513 Z= 0.168 Angle : 0.655 14.801 11551 Z= 0.338 Chirality : 0.045 0.211 1287 Planarity : 0.005 0.066 1465 Dihedral : 7.280 155.801 1156 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.87 % Allowed : 20.99 % Favored : 76.13 % 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: 1.41 (0.27), residues: 391 sheet: 0.03 (0.31), residues: 239 loop : -0.79 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.026 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 covalent geometry : bond 0.00380 ( 8509) covalent geometry : angle 0.65142 (11543) SS BOND : bond 0.00119 ( 4) SS BOND : angle 2.66740 ( 8) hydrogen bonds : bond 0.04792 ( 409) hydrogen bonds : angle 4.66033 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4062.61 seconds wall clock time: 69 minutes 48.03 seconds (4188.03 seconds total)