Starting phenix.real_space_refine on Sat Jun 7 03:27:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmp_34902/06_2025/8hmp_34902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmp_34902/06_2025/8hmp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hmp_34902/06_2025/8hmp_34902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmp_34902/06_2025/8hmp_34902.map" model { file = "/net/cci-nas-00/data/ceres_data/8hmp_34902/06_2025/8hmp_34902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmp_34902/06_2025/8hmp_34902.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.52, per 1000 atoms: 0.90 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: 2.02 Conformation dependent library (CDL) restraints added in 936.5 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: 0.87 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: 2.43 Time building geometry restraints manager: 2.40 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: 9.350 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- 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 : 5.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (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 TRP 0.049 0.003 TRP R 278 HIS 0.011 0.001 HIS A 357 PHE 0.024 0.002 PHE N 108 TYR 0.062 0.003 TYR B 59 ARG 0.008 0.001 ARG R 291 Details of bonding type rmsd hydrogen bonds : bond 0.13521 ( 409) hydrogen bonds : angle 5.99898 ( 1182) SS BOND : bond 0.00557 ( 4) SS BOND : angle 1.59977 ( 8) covalent geometry : bond 0.00517 ( 8509) covalent geometry : angle 0.91867 (11543) *********************** 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 : 0.885 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: 0.7294 (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: 1.1836 time to fit residues: 305.3709 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 : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148650 restraints weight = 9432.827| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.11 r_work: 0.3628 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8513 Z= 0.216 Angle : 0.685 15.574 11551 Z= 0.359 Chirality : 0.047 0.162 1287 Planarity : 0.005 0.065 1465 Dihedral : 7.660 153.635 1156 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.54 % Allowed : 11.38 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1031 helix: 1.01 (0.26), residues: 388 sheet: 0.10 (0.32), residues: 233 loop : -0.95 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.010 0.002 HIS A 357 PHE 0.021 0.002 PHE A 212 TYR 0.032 0.002 TYR B 59 ARG 0.005 0.001 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.05711 ( 409) hydrogen bonds : angle 4.93165 ( 1182) SS BOND : bond 0.00372 ( 4) SS BOND : angle 2.17346 ( 8) covalent geometry : bond 0.00482 ( 8509) covalent geometry : angle 0.68267 (11543) *********************** 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 228 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.993 Fit side-chains REVERT: B 59 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: B 219 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7224 (mmm-85) REVERT: N 73 ASP cc_start: 0.8051 (m-30) cc_final: 0.7748 (m-30) REVERT: N 80 TYR cc_start: 0.8652 (m-80) cc_final: 0.8444 (m-80) REVERT: R 137 VAL cc_start: 0.8748 (p) cc_final: 0.7874 (m) REVERT: R 212 TYR cc_start: 0.7219 (m-80) cc_final: 0.6956 (m-10) REVERT: R 235 LYS cc_start: 0.7566 (tppp) cc_final: 0.7287 (tptp) REVERT: R 265 MET cc_start: 0.5443 (tmm) cc_final: 0.4113 (mtt) REVERT: A 25 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8127 (ttmp) REVERT: A 35 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: A 61 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6536 (mtt180) REVERT: A 253 TYR cc_start: 0.8579 (m-80) cc_final: 0.8301 (m-80) REVERT: A 343 ASP cc_start: 0.8429 (m-30) cc_final: 0.8119 (m-30) REVERT: A 370 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7456 (mp0) outliers start: 23 outliers final: 11 residues processed: 211 average time/residue: 1.2318 time to fit residues: 276.2650 Evaluate side-chains 196 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 266 HIS N 77 ASN R 151 GLN A 14 ASN A 362 HIS 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 = 0.189831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149211 restraints weight = 9529.245| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.13 r_work: 0.3641 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8513 Z= 0.168 Angle : 0.632 15.469 11551 Z= 0.326 Chirality : 0.045 0.166 1287 Planarity : 0.005 0.053 1465 Dihedral : 7.523 156.916 1156 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.43 % Allowed : 13.81 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1031 helix: 1.38 (0.26), residues: 388 sheet: 0.07 (0.32), residues: 231 loop : -0.96 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.025 0.002 TYR B 59 ARG 0.005 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 409) hydrogen bonds : angle 4.73361 ( 1182) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.59460 ( 8) covalent geometry : bond 0.00371 ( 8509) covalent geometry : angle 0.63048 (11543) *********************** 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 226 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7583 (m-10) REVERT: B 219 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7139 (mmm-85) REVERT: N 73 ASP cc_start: 0.8058 (m-30) cc_final: 0.7716 (m-30) REVERT: N 80 TYR cc_start: 0.8649 (m-80) cc_final: 0.8393 (m-80) REVERT: R 137 VAL cc_start: 0.8737 (p) cc_final: 0.7858 (m) REVERT: R 143 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8248 (tp) REVERT: R 190 PHE cc_start: 0.8102 (m-80) cc_final: 0.7862 (m-80) REVERT: R 212 TYR cc_start: 0.7169 (m-80) cc_final: 0.6834 (m-80) REVERT: R 235 LYS cc_start: 0.7642 (tppp) cc_final: 0.7294 (tptp) REVERT: R 265 MET cc_start: 0.5403 (tmm) cc_final: 0.4054 (mtt) REVERT: A 25 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8102 (ttmp) REVERT: A 35 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: A 253 TYR cc_start: 0.8614 (m-80) cc_final: 0.8361 (m-80) REVERT: A 370 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7415 (mp0) outliers start: 31 outliers final: 17 residues processed: 211 average time/residue: 1.1599 time to fit residues: 260.3679 Evaluate side-chains 202 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 241 VAL 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 52 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.0040 chunk 93 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 151 GLN A 14 ASN A 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.191339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150980 restraints weight = 9474.930| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.11 r_work: 0.3660 rms_B_bonded: 2.85 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: 0.8042 moved from start: 0.1871 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= 0.138 Angle : 0.585 14.582 11551 Z= 0.305 Chirality : 0.044 0.164 1287 Planarity : 0.004 0.051 1465 Dihedral : 7.338 156.342 1156 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.31 % Allowed : 15.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1031 helix: 1.53 (0.26), residues: 388 sheet: 0.06 (0.31), residues: 231 loop : -0.96 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.022 0.002 TYR R 284 ARG 0.004 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 409) hydrogen bonds : angle 4.59161 ( 1182) SS BOND : bond 0.00272 ( 4) SS BOND : angle 2.28267 ( 8) covalent geometry : bond 0.00301 ( 8509) covalent geometry : angle 0.58175 (11543) *********************** 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 219 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: B 219 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7324 (mmm-85) REVERT: N 53 GLN cc_start: 0.8078 (mp10) cc_final: 0.7877 (mp10) REVERT: N 73 ASP cc_start: 0.8031 (m-30) cc_final: 0.7706 (m-30) REVERT: N 80 TYR cc_start: 0.8637 (m-80) cc_final: 0.8376 (m-80) REVERT: R 137 VAL cc_start: 0.8701 (p) cc_final: 0.7819 (m) REVERT: R 143 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8179 (tp) REVERT: R 190 PHE cc_start: 0.8103 (m-80) cc_final: 0.7740 (m-80) REVERT: R 235 LYS cc_start: 0.7629 (tppp) cc_final: 0.7290 (tptp) REVERT: R 265 MET cc_start: 0.5402 (tmm) cc_final: 0.3999 (mtt) REVERT: R 284 TYR cc_start: 0.8316 (t80) cc_final: 0.8019 (t80) REVERT: A 25 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8052 (ttmp) REVERT: A 35 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: A 253 TYR cc_start: 0.8635 (m-80) cc_final: 0.8428 (m-80) REVERT: A 370 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7444 (mp0) outliers start: 30 outliers final: 18 residues processed: 204 average time/residue: 1.1438 time to fit residues: 248.6813 Evaluate side-chains 198 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 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 164 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 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 0 optimal weight: 40.0000 chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.189276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149194 restraints weight = 9430.292| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.09 r_work: 0.3633 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8513 Z= 0.181 Angle : 0.622 15.037 11551 Z= 0.326 Chirality : 0.045 0.168 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.421 156.053 1156 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.76 % Allowed : 16.02 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1031 helix: 1.36 (0.26), residues: 389 sheet: 0.03 (0.31), residues: 232 loop : -0.95 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.027 0.002 TYR B 59 ARG 0.005 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 409) hydrogen bonds : angle 4.71377 ( 1182) SS BOND : bond 0.00172 ( 4) SS BOND : angle 4.01983 ( 8) covalent geometry : bond 0.00404 ( 8509) covalent geometry : angle 0.61316 (11543) *********************** 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: 34 poor density : 188 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: B 197 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6734 (mtm110) REVERT: B 219 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7300 (mmm-85) REVERT: B 262 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8015 (mpt) REVERT: N 73 ASP cc_start: 0.8075 (m-30) cc_final: 0.7798 (m-30) REVERT: N 80 TYR cc_start: 0.8653 (m-80) cc_final: 0.8439 (m-80) REVERT: R 137 VAL cc_start: 0.8762 (p) cc_final: 0.8550 (t) REVERT: R 143 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8252 (tp) REVERT: R 190 PHE cc_start: 0.8164 (m-80) cc_final: 0.7948 (m-80) REVERT: R 212 TYR cc_start: 0.7303 (m-80) cc_final: 0.6979 (m-80) REVERT: R 235 LYS cc_start: 0.7636 (tppp) cc_final: 0.7316 (tptp) REVERT: R 265 MET cc_start: 0.5463 (tmm) cc_final: 0.4089 (mtt) REVERT: R 284 TYR cc_start: 0.8328 (t80) cc_final: 0.8046 (t80) REVERT: A 35 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: A 59 GLN cc_start: 0.6050 (OUTLIER) cc_final: 0.5540 (mt0) REVERT: A 370 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7481 (mp0) REVERT: A 386 MET cc_start: 0.7176 (mtp) cc_final: 0.6656 (mtt) outliers start: 34 outliers final: 20 residues processed: 207 average time/residue: 1.1849 time to fit residues: 260.9767 Evaluate side-chains 211 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 164 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 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 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.188317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148184 restraints weight = 9470.283| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.08 r_work: 0.3628 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8513 Z= 0.201 Angle : 0.661 16.018 11551 Z= 0.344 Chirality : 0.046 0.194 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.490 155.354 1156 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.20 % Allowed : 17.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1031 helix: 1.26 (0.26), residues: 390 sheet: -0.03 (0.31), residues: 232 loop : -1.00 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.028 0.002 TYR B 59 ARG 0.004 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 409) hydrogen bonds : angle 4.80536 ( 1182) SS BOND : bond 0.00414 ( 4) SS BOND : angle 3.98269 ( 8) covalent geometry : bond 0.00453 ( 8509) covalent geometry : angle 0.65319 (11543) *********************** 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 226 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: B 197 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6611 (mtm110) REVERT: B 219 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7218 (mmm-85) REVERT: B 262 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7997 (mpt) REVERT: G 18 GLN cc_start: 0.4417 (OUTLIER) cc_final: 0.4071 (tp-100) REVERT: N 73 ASP cc_start: 0.8062 (m-30) cc_final: 0.7783 (m-30) REVERT: R 137 VAL cc_start: 0.8792 (p) cc_final: 0.8586 (t) REVERT: R 143 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8271 (tp) REVERT: R 212 TYR cc_start: 0.7329 (m-80) cc_final: 0.7057 (m-80) REVERT: R 235 LYS cc_start: 0.7631 (tppp) cc_final: 0.7388 (tppp) REVERT: R 265 MET cc_start: 0.5513 (tmm) cc_final: 0.4150 (mtt) REVERT: R 276 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: R 284 TYR cc_start: 0.8323 (t80) cc_final: 0.8006 (t80) REVERT: A 35 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: A 370 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7460 (mp0) REVERT: A 386 MET cc_start: 0.7187 (mtp) cc_final: 0.6735 (mtt) outliers start: 38 outliers final: 24 residues processed: 209 average time/residue: 1.3653 time to fit residues: 302.9146 Evaluate side-chains 216 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 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 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 36 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 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 276 MET 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 241 VAL Chi-restraints excluded: chain A residue 254 ASN 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 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 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 G 18 GLN N 77 ASN R 151 GLN A 14 ASN A 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.189479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149663 restraints weight = 9472.243| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.08 r_work: 0.3645 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8513 Z= 0.168 Angle : 0.641 15.295 11551 Z= 0.333 Chirality : 0.045 0.196 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.403 155.109 1156 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.87 % Allowed : 18.23 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1031 helix: 1.33 (0.27), residues: 389 sheet: -0.03 (0.31), residues: 234 loop : -0.98 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.025 0.002 TYR B 59 ARG 0.004 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 409) hydrogen bonds : angle 4.78639 ( 1182) SS BOND : bond 0.00165 ( 4) SS BOND : angle 3.34863 ( 8) covalent geometry : bond 0.00377 ( 8509) covalent geometry : angle 0.63500 (11543) *********************** 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 227 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7714 (m-10) REVERT: B 197 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6536 (mtm110) REVERT: B 219 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7281 (mmm-85) REVERT: B 262 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8020 (mpt) REVERT: N 73 ASP cc_start: 0.8028 (m-30) cc_final: 0.7772 (m-30) REVERT: N 80 TYR cc_start: 0.8648 (m-80) cc_final: 0.8432 (m-80) REVERT: R 137 VAL cc_start: 0.8770 (p) cc_final: 0.8553 (t) REVERT: R 143 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8260 (tp) REVERT: R 212 TYR cc_start: 0.7318 (m-80) cc_final: 0.7056 (m-80) REVERT: R 265 MET cc_start: 0.5469 (tmm) cc_final: 0.4104 (mtt) REVERT: R 276 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8045 (mpp) REVERT: R 284 TYR cc_start: 0.8293 (t80) cc_final: 0.7972 (t80) REVERT: A 16 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 20 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7162 (mtp85) REVERT: A 35 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: A 370 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7459 (mp0) REVERT: A 386 MET cc_start: 0.7186 (mtp) cc_final: 0.6731 (mtt) outliers start: 35 outliers final: 19 residues processed: 212 average time/residue: 1.1361 time to fit residues: 256.6876 Evaluate side-chains 208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 36 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 164 LEU Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 276 MET 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 241 VAL Chi-restraints excluded: chain A residue 254 ASN 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 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 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 = 0.192217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152616 restraints weight = 9501.996| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.08 r_work: 0.3674 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8513 Z= 0.132 Angle : 0.616 13.850 11551 Z= 0.320 Chirality : 0.044 0.194 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.252 155.243 1156 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.76 % Allowed : 18.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1031 helix: 1.38 (0.27), residues: 391 sheet: 0.00 (0.31), residues: 234 loop : -0.93 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.022 0.002 TYR R 284 ARG 0.004 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 409) hydrogen bonds : angle 4.66286 ( 1182) SS BOND : bond 0.00147 ( 4) SS BOND : angle 3.21121 ( 8) covalent geometry : bond 0.00289 ( 8509) covalent geometry : angle 0.61017 (11543) *********************** 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 223 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7436 (m-10) REVERT: B 219 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7276 (mmm-85) REVERT: B 262 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8043 (mpt) REVERT: N 73 ASP cc_start: 0.8056 (m-30) cc_final: 0.7790 (m-30) REVERT: N 77 ASN cc_start: 0.8269 (m-40) cc_final: 0.8055 (m110) REVERT: N 80 TYR cc_start: 0.8600 (m-80) cc_final: 0.8374 (m-80) REVERT: R 137 VAL cc_start: 0.8684 (p) cc_final: 0.7802 (m) REVERT: R 212 TYR cc_start: 0.7297 (m-80) cc_final: 0.7006 (m-80) REVERT: R 265 MET cc_start: 0.5436 (tmm) cc_final: 0.4047 (mtt) REVERT: R 284 TYR cc_start: 0.8264 (t80) cc_final: 0.7934 (t80) REVERT: A 35 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: A 370 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7500 (mp0) outliers start: 34 outliers final: 18 residues processed: 210 average time/residue: 1.1790 time to fit residues: 264.6200 Evaluate side-chains 205 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 158 LEU Chi-restraints excluded: chain R residue 164 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 241 VAL Chi-restraints excluded: chain A residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN R 151 GLN A 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.190868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151125 restraints weight = 9506.423| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.10 r_work: 0.3649 rms_B_bonded: 2.87 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: 0.8085 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8513 Z= 0.159 Angle : 0.651 14.922 11551 Z= 0.340 Chirality : 0.045 0.203 1287 Planarity : 0.004 0.054 1465 Dihedral : 7.325 155.581 1156 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.54 % Allowed : 20.88 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1031 helix: 1.32 (0.27), residues: 391 sheet: 0.09 (0.32), residues: 232 loop : -0.94 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.024 0.002 TYR B 59 ARG 0.005 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 409) hydrogen bonds : angle 4.73245 ( 1182) SS BOND : bond 0.00228 ( 4) SS BOND : angle 3.07345 ( 8) covalent geometry : bond 0.00359 ( 8509) covalent geometry : angle 0.64637 (11543) *********************** 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 211 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7637 (m-10) REVERT: B 219 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7252 (mmm-85) REVERT: B 262 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8070 (mpt) REVERT: N 73 ASP cc_start: 0.8024 (m-30) cc_final: 0.7782 (m-30) REVERT: N 77 ASN cc_start: 0.8286 (m-40) cc_final: 0.8056 (m110) REVERT: N 80 TYR cc_start: 0.8636 (m-80) cc_final: 0.8431 (m-80) REVERT: R 137 VAL cc_start: 0.8723 (p) cc_final: 0.8509 (t) REVERT: R 212 TYR cc_start: 0.7301 (m-80) cc_final: 0.7041 (m-80) REVERT: R 243 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7755 (ttt180) REVERT: R 265 MET cc_start: 0.5403 (tmm) cc_final: 0.4031 (mtt) REVERT: R 284 TYR cc_start: 0.8262 (t80) cc_final: 0.7930 (t80) REVERT: R 286 LEU cc_start: 0.8853 (mm) cc_final: 0.8619 (mm) REVERT: A 16 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6979 (tm-30) REVERT: A 20 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7111 (mtp85) REVERT: A 35 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: A 370 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7449 (mp0) outliers start: 23 outliers final: 16 residues processed: 205 average time/residue: 1.2759 time to fit residues: 279.5994 Evaluate side-chains 200 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 164 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 241 VAL Chi-restraints excluded: chain A residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.192301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152120 restraints weight = 9441.714| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.13 r_work: 0.3641 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8513 Z= 0.158 Angle : 0.662 14.866 11551 Z= 0.343 Chirality : 0.045 0.205 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.311 155.195 1156 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.76 % Allowed : 20.88 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1031 helix: 1.28 (0.27), residues: 391 sheet: 0.03 (0.31), residues: 234 loop : -0.91 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.030 0.002 TYR B 59 ARG 0.005 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 409) hydrogen bonds : angle 4.75677 ( 1182) SS BOND : bond 0.00129 ( 4) SS BOND : angle 2.83715 ( 8) covalent geometry : bond 0.00357 ( 8509) covalent geometry : angle 0.65846 (11543) ********************** 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 208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7540 (m-10) REVERT: B 219 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7177 (mmm-85) REVERT: B 262 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8056 (mpt) REVERT: N 73 ASP cc_start: 0.8036 (m-30) cc_final: 0.7784 (m-30) REVERT: N 80 TYR cc_start: 0.8637 (m-80) cc_final: 0.8434 (m-80) REVERT: R 115 GLN cc_start: 0.8622 (mp10) cc_final: 0.8321 (mp10) REVERT: R 137 VAL cc_start: 0.8703 (p) cc_final: 0.8480 (t) REVERT: R 143 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8211 (tp) REVERT: R 212 TYR cc_start: 0.7252 (m-80) cc_final: 0.6996 (m-80) REVERT: R 243 ARG cc_start: 0.7943 (ttt180) cc_final: 0.7741 (ttt180) REVERT: R 265 MET cc_start: 0.5351 (tmm) cc_final: 0.3988 (mtt) REVERT: R 284 TYR cc_start: 0.8260 (t80) cc_final: 0.7942 (t80) REVERT: R 286 LEU cc_start: 0.8869 (mm) cc_final: 0.8629 (mm) REVERT: A 35 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8228 (mp10) outliers start: 25 outliers final: 17 residues processed: 201 average time/residue: 1.1428 time to fit residues: 245.3434 Evaluate side-chains 200 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 63 SER 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 164 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 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 0 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 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 = 0.4233 r_free = 0.4233 target = 0.194132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154312 restraints weight = 9496.814| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.14 r_work: 0.3670 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8513 Z= 0.139 Angle : 0.641 14.067 11551 Z= 0.332 Chirality : 0.044 0.203 1287 Planarity : 0.004 0.053 1465 Dihedral : 7.219 154.901 1156 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.65 % Allowed : 20.99 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1031 helix: 1.34 (0.27), residues: 391 sheet: 0.14 (0.31), residues: 231 loop : -0.88 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.028 0.002 TYR B 59 ARG 0.004 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 409) hydrogen bonds : angle 4.66730 ( 1182) SS BOND : bond 0.00100 ( 4) SS BOND : angle 2.45595 ( 8) covalent geometry : bond 0.00312 ( 8509) covalent geometry : angle 0.63813 (11543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9532.84 seconds wall clock time: 167 minutes 4.82 seconds (10024.82 seconds total)