Starting phenix.real_space_refine on Wed Sep 25 03:30:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/09_2024/7dur_30867.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/09_2024/7dur_30867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/09_2024/7dur_30867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/09_2024/7dur_30867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/09_2024/7dur_30867.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/09_2024/7dur_30867.cif" } resolution = 3.3 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= -0.001 sd= 0.017 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 54 5.16 5 Cl 2 4.86 5 C 5920 2.51 5 N 1571 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1957 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 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: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} 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: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3079 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 14, 'TRANS': 356} Chain breaks: 4 Chain: "R" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 185 Unusual residues: {'CLR': 6, 'HNO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.69, per 1000 atoms: 0.62 Number of scatterers: 9211 At special positions: 0 Unit cell: (94.05, 95.095, 156.75, 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) Cl 2 17.00 S 54 16.00 O 1664 8.00 N 1571 7.00 C 5920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.9% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 4.262A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.770A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.904A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.834A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.689A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.911A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 53 removed outlier: 3.663A pdb=" N VAL R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 123 through 127 removed outlier: 4.281A pdb=" N CYS R 126 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.810A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 212 removed outlier: 4.007A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 222 Processing helix chain 'R' and resid 223 through 257 removed outlier: 4.200A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 292 removed outlier: 3.604A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.596A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 removed outlier: 3.843A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 368 removed outlier: 4.303A pdb=" N PHE R 367 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 404 removed outlier: 4.162A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.006A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.939A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.859A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.747A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.201A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.945A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.578A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 82 through 84 removed outlier: 3.549A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1302 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: 2.77 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2886 1.34 - 1.46: 2043 1.46 - 1.58: 4430 1.58 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 9434 Sorted by residual: bond pdb=" C14 HNO R 701 " pdb=" N15 HNO R 701 " ideal model delta sigma weight residual 1.348 1.458 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" CA GLU A 314 " pdb=" C GLU A 314 " ideal model delta sigma weight residual 1.522 1.447 0.074 1.72e-02 3.38e+03 1.87e+01 bond pdb=" N LEU R 32 " pdb=" CA LEU R 32 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.40e-02 5.10e+03 9.53e+00 bond pdb=" C20 HNO R 701 " pdb=" C21 HNO R 701 " ideal model delta sigma weight residual 1.418 1.359 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" CA SER R 31 " pdb=" C SER R 31 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.34e-02 5.57e+03 8.34e+00 ... (remaining 9429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12196 2.27 - 4.54: 532 4.54 - 6.82: 72 6.82 - 9.09: 17 9.09 - 11.36: 6 Bond angle restraints: 12823 Sorted by residual: angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 113.15 103.96 9.19 1.19e+00 7.06e-01 5.97e+01 angle pdb=" N HIS R 212 " pdb=" CA HIS R 212 " pdb=" C HIS R 212 " ideal model delta sigma weight residual 111.74 104.59 7.15 1.35e+00 5.49e-01 2.80e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 117.19 3.05 6.30e-01 2.52e+00 2.34e+01 angle pdb=" CA TRP A 277 " pdb=" CB TRP A 277 " pdb=" CG TRP A 277 " ideal model delta sigma weight residual 113.60 105.95 7.65 1.90e+00 2.77e-01 1.62e+01 angle pdb=" C THR A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 122.82 128.08 -5.26 1.42e+00 4.96e-01 1.37e+01 ... (remaining 12818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5168 17.88 - 35.75: 517 35.75 - 53.63: 131 53.63 - 71.50: 42 71.50 - 89.38: 8 Dihedral angle restraints: 5866 sinusoidal: 2581 harmonic: 3285 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 27.19 65.81 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 151.70 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -44.74 -41.26 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 5863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1267 0.095 - 0.190: 138 0.190 - 0.285: 13 0.285 - 0.381: 6 0.381 - 0.476: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CG LEU R 32 " pdb=" CB LEU R 32 " pdb=" CD1 LEU R 32 " pdb=" CD2 LEU R 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C14 CLR R 703 " pdb=" C13 CLR R 703 " pdb=" C15 CLR R 703 " pdb=" C8 CLR R 703 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1423 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 372 " 0.023 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ILE A 372 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE A 372 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 373 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 410 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLN R 410 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN R 410 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU R 411 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 30 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.89e+00 pdb=" C VAL R 30 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL R 30 " 0.021 2.00e-02 2.50e+03 pdb=" N SER R 31 " 0.018 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 142 2.62 - 3.19: 8414 3.19 - 3.76: 15160 3.76 - 4.33: 21067 4.33 - 4.90: 33311 Nonbonded interactions: 78094 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.048 3.040 nonbonded pdb=" O TRP R 91 " pdb=" OG SER R 94 " model vdw 2.112 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS A 271 " pdb=" OD2 ASP N 50 " model vdw 2.242 3.120 ... (remaining 78089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 : 0.008 0.110 9434 Z= 0.496 Angle : 1.094 11.361 12823 Z= 0.593 Chirality : 0.066 0.476 1426 Planarity : 0.007 0.055 1593 Dihedral : 15.688 89.376 3722 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.61 % Allowed : 7.79 % Favored : 87.60 % 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: -2.47 (0.23), residues: 1104 helix: -1.79 (0.21), residues: 433 sheet: -1.25 (0.32), residues: 201 loop : -1.46 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP R 87 HIS 0.011 0.002 HIS B 142 PHE 0.053 0.004 PHE R 280 TYR 0.034 0.004 TYR B 264 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 250 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8891 (p0) REVERT: B 217 MET cc_start: 0.6367 (ptt) cc_final: 0.5314 (ptt) REVERT: B 264 TYR cc_start: 0.5898 (m-80) cc_final: 0.4706 (m-80) REVERT: G 38 MET cc_start: 0.8543 (ptt) cc_final: 0.7896 (ptt) REVERT: N 80 TYR cc_start: 0.6765 (m-80) cc_final: 0.6438 (m-80) REVERT: N 81 LEU cc_start: 0.8637 (tp) cc_final: 0.8373 (pp) REVERT: R 48 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5159 (ptt90) REVERT: R 146 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8743 (tp) REVERT: R 147 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (mt) REVERT: R 203 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8599 (t60) REVERT: R 311 LEU cc_start: 0.8624 (tt) cc_final: 0.8378 (mm) REVERT: R 393 PHE cc_start: 0.8781 (m-80) cc_final: 0.8037 (m-10) REVERT: R 410 GLN cc_start: 0.8719 (mt0) cc_final: 0.8484 (mt0) REVERT: R 421 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8047 (mmp-170) outliers start: 45 outliers final: 15 residues processed: 284 average time/residue: 0.2597 time to fit residues: 95.9934 Evaluate side-chains 151 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 39 TRP Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 48 ARG Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 203 TRP Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 416 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9434 Z= 0.256 Angle : 0.740 7.830 12823 Z= 0.387 Chirality : 0.046 0.170 1426 Planarity : 0.005 0.043 1593 Dihedral : 9.449 77.575 1672 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.92 % Allowed : 15.68 % Favored : 79.41 % 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: -1.17 (0.24), residues: 1104 helix: -0.28 (0.24), residues: 427 sheet: -0.85 (0.31), residues: 220 loop : -1.06 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 36 HIS 0.008 0.001 HIS B 225 PHE 0.031 0.002 PHE N 29 TYR 0.039 0.002 TYR N 32 ARG 0.007 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 154 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8283 (mm110) cc_final: 0.7901 (mm110) REVERT: B 188 MET cc_start: 0.6890 (mmp) cc_final: 0.6645 (mmp) REVERT: B 264 TYR cc_start: 0.5828 (m-80) cc_final: 0.5523 (m-80) REVERT: B 296 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7164 (m) REVERT: G 38 MET cc_start: 0.8572 (ptt) cc_final: 0.8220 (ptm) REVERT: R 221 GLN cc_start: 0.8835 (mm110) cc_final: 0.8441 (pp30) REVERT: R 269 TYR cc_start: 0.7822 (m-80) cc_final: 0.7265 (m-80) REVERT: R 353 THR cc_start: 0.9531 (m) cc_final: 0.9293 (p) REVERT: R 393 PHE cc_start: 0.8764 (m-80) cc_final: 0.8382 (m-10) REVERT: R 418 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8385 (mm-30) outliers start: 48 outliers final: 28 residues processed: 187 average time/residue: 0.2138 time to fit residues: 55.0383 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9434 Z= 0.268 Angle : 0.701 11.662 12823 Z= 0.363 Chirality : 0.045 0.186 1426 Planarity : 0.004 0.040 1593 Dihedral : 8.115 71.354 1641 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.71 % Allowed : 18.55 % Favored : 76.74 % 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: -0.78 (0.24), residues: 1104 helix: 0.14 (0.24), residues: 436 sheet: -0.70 (0.34), residues: 212 loop : -0.92 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 36 HIS 0.006 0.001 HIS B 225 PHE 0.019 0.002 PHE R 280 TYR 0.020 0.002 TYR R 148 ARG 0.013 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 133 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7373 (m) REVERT: B 336 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7705 (tp) REVERT: G 32 LYS cc_start: 0.9304 (tmtt) cc_final: 0.9078 (tmmt) REVERT: G 38 MET cc_start: 0.8585 (ptt) cc_final: 0.8357 (ptm) REVERT: N 81 LEU cc_start: 0.8554 (pp) cc_final: 0.8311 (pp) REVERT: R 269 TYR cc_start: 0.7848 (m-80) cc_final: 0.7417 (m-80) REVERT: R 393 PHE cc_start: 0.8789 (m-80) cc_final: 0.8415 (m-10) REVERT: R 415 LYS cc_start: 0.9214 (ptpt) cc_final: 0.8971 (pttm) outliers start: 46 outliers final: 30 residues processed: 165 average time/residue: 0.2052 time to fit residues: 47.6173 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.0170 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9434 Z= 0.183 Angle : 0.661 10.684 12823 Z= 0.337 Chirality : 0.043 0.173 1426 Planarity : 0.004 0.035 1593 Dihedral : 7.470 59.830 1633 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.10 % Allowed : 21.11 % Favored : 74.80 % 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: -0.33 (0.25), residues: 1104 helix: 0.54 (0.24), residues: 424 sheet: -0.34 (0.35), residues: 201 loop : -0.75 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 36 HIS 0.012 0.001 HIS A 220 PHE 0.020 0.002 PHE R 230 TYR 0.017 0.002 TYR R 148 ARG 0.009 0.000 ARG R 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6564 (m-80) cc_final: 0.6336 (m-80) REVERT: B 264 TYR cc_start: 0.5941 (m-80) cc_final: 0.5160 (m-80) REVERT: B 296 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7407 (m) REVERT: G 32 LYS cc_start: 0.9312 (tmtt) cc_final: 0.9079 (tmmt) REVERT: G 38 MET cc_start: 0.8634 (ptt) cc_final: 0.8279 (ptm) REVERT: N 93 VAL cc_start: 0.8346 (p) cc_final: 0.8040 (t) REVERT: N 123 GLN cc_start: 0.7491 (tp-100) cc_final: 0.6923 (tp40) REVERT: R 269 TYR cc_start: 0.7776 (m-80) cc_final: 0.7306 (m-80) REVERT: R 393 PHE cc_start: 0.8657 (m-80) cc_final: 0.8286 (m-80) outliers start: 40 outliers final: 27 residues processed: 177 average time/residue: 0.2035 time to fit residues: 51.2512 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 90 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9434 Z= 0.204 Angle : 0.656 12.533 12823 Z= 0.332 Chirality : 0.044 0.157 1426 Planarity : 0.004 0.033 1593 Dihedral : 7.030 59.883 1627 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.51 % Allowed : 21.72 % Favored : 73.77 % 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 (0.25), residues: 1104 helix: 0.60 (0.24), residues: 436 sheet: -0.19 (0.35), residues: 186 loop : -0.75 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 36 HIS 0.004 0.001 HIS A 362 PHE 0.027 0.002 PHE A 219 TYR 0.016 0.002 TYR R 148 ARG 0.009 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5240 (pp30) REVERT: B 264 TYR cc_start: 0.6309 (m-80) cc_final: 0.5991 (m-80) REVERT: B 296 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7406 (m) REVERT: G 32 LYS cc_start: 0.9300 (tmtt) cc_final: 0.9078 (tmmt) REVERT: G 38 MET cc_start: 0.8616 (ptt) cc_final: 0.8398 (ptm) REVERT: R 179 ILE cc_start: 0.9134 (mm) cc_final: 0.8830 (mm) REVERT: R 221 GLN cc_start: 0.8770 (mm110) cc_final: 0.8169 (tm-30) REVERT: R 269 TYR cc_start: 0.7627 (m-80) cc_final: 0.7270 (m-80) REVERT: R 393 PHE cc_start: 0.8538 (m-80) cc_final: 0.8223 (m-80) outliers start: 44 outliers final: 33 residues processed: 164 average time/residue: 0.1883 time to fit residues: 44.2350 Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9434 Z= 0.180 Angle : 0.655 11.752 12823 Z= 0.327 Chirality : 0.043 0.214 1426 Planarity : 0.004 0.034 1593 Dihedral : 6.806 59.746 1627 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.79 % Allowed : 23.16 % Favored : 73.05 % 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: 0.09 (0.25), residues: 1104 helix: 0.92 (0.25), residues: 428 sheet: -0.08 (0.35), residues: 202 loop : -0.58 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE A 219 TYR 0.019 0.002 TYR B 264 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 GLU cc_start: 0.5338 (mp0) cc_final: 0.4359 (mt-10) REVERT: B 246 ASP cc_start: 0.8573 (t0) cc_final: 0.8323 (t0) REVERT: B 296 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7252 (m) REVERT: G 32 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9133 (tmmt) REVERT: G 38 MET cc_start: 0.8634 (ptt) cc_final: 0.8392 (ptm) REVERT: N 93 VAL cc_start: 0.8689 (t) cc_final: 0.7960 (p) REVERT: R 221 GLN cc_start: 0.8814 (mm110) cc_final: 0.8193 (tm-30) REVERT: R 269 TYR cc_start: 0.7512 (m-80) cc_final: 0.7246 (m-80) REVERT: R 393 PHE cc_start: 0.8577 (m-80) cc_final: 0.8145 (m-80) outliers start: 37 outliers final: 31 residues processed: 164 average time/residue: 0.2345 time to fit residues: 54.4923 Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9434 Z= 0.234 Angle : 0.665 10.133 12823 Z= 0.337 Chirality : 0.044 0.195 1426 Planarity : 0.004 0.031 1593 Dihedral : 6.591 59.806 1627 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.51 % Allowed : 24.18 % Favored : 71.31 % 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: 0.10 (0.25), residues: 1104 helix: 0.96 (0.25), residues: 435 sheet: -0.16 (0.36), residues: 195 loop : -0.59 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 36 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE R 280 TYR 0.016 0.002 TYR R 148 ARG 0.005 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.5509 (pp30) REVERT: B 226 GLU cc_start: 0.5705 (mp0) cc_final: 0.4707 (mt-10) REVERT: B 296 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7582 (m) REVERT: G 32 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9193 (tmmt) REVERT: R 221 GLN cc_start: 0.8885 (mm110) cc_final: 0.8223 (tm-30) REVERT: R 269 TYR cc_start: 0.7663 (m-80) cc_final: 0.7323 (m-80) REVERT: R 393 PHE cc_start: 0.8572 (m-80) cc_final: 0.8191 (m-80) outliers start: 44 outliers final: 36 residues processed: 158 average time/residue: 0.1948 time to fit residues: 44.2977 Evaluate side-chains 150 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9434 Z= 0.236 Angle : 0.685 14.195 12823 Z= 0.342 Chirality : 0.044 0.150 1426 Planarity : 0.004 0.035 1593 Dihedral : 6.393 58.878 1627 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.82 % Allowed : 23.67 % Favored : 71.52 % 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: 1104 helix: 1.12 (0.25), residues: 429 sheet: -0.04 (0.36), residues: 196 loop : -0.49 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP N 36 HIS 0.005 0.001 HIS A 362 PHE 0.016 0.002 PHE R 280 TYR 0.021 0.002 TYR B 59 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5613 (pp30) REVERT: A 216 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6209 (pttp) REVERT: B 296 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7593 (m) REVERT: G 32 LYS cc_start: 0.9431 (tmtt) cc_final: 0.9228 (tmmt) REVERT: R 221 GLN cc_start: 0.8916 (mm110) cc_final: 0.8244 (tm-30) REVERT: R 269 TYR cc_start: 0.7672 (m-80) cc_final: 0.7370 (m-80) REVERT: R 393 PHE cc_start: 0.8526 (m-80) cc_final: 0.8158 (m-80) outliers start: 47 outliers final: 36 residues processed: 161 average time/residue: 0.2017 time to fit residues: 45.4340 Evaluate side-chains 153 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 394 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9434 Z= 0.187 Angle : 0.709 13.035 12823 Z= 0.347 Chirality : 0.044 0.285 1426 Planarity : 0.004 0.032 1593 Dihedral : 6.185 56.838 1627 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.59 % Allowed : 25.41 % Favored : 71.00 % 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: 0.36 (0.26), residues: 1104 helix: 1.24 (0.25), residues: 429 sheet: -0.04 (0.36), residues: 203 loop : -0.48 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 36 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE R 280 TYR 0.022 0.002 TYR N 94 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7883 (mm-30) REVERT: R 221 GLN cc_start: 0.8860 (mm110) cc_final: 0.8257 (tm-30) REVERT: R 269 TYR cc_start: 0.7598 (m-80) cc_final: 0.7319 (m-80) REVERT: R 393 PHE cc_start: 0.8473 (m-80) cc_final: 0.8107 (m-80) outliers start: 35 outliers final: 31 residues processed: 151 average time/residue: 0.2040 time to fit residues: 43.7082 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9434 Z= 0.210 Angle : 0.744 14.119 12823 Z= 0.367 Chirality : 0.045 0.261 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.112 54.560 1627 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.69 % Allowed : 25.51 % Favored : 70.80 % 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 (0.26), residues: 1104 helix: 1.28 (0.25), residues: 429 sheet: -0.12 (0.36), residues: 204 loop : -0.57 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP N 36 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 280 TYR 0.018 0.002 TYR N 94 ARG 0.015 0.001 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.5505 (pp30) REVERT: A 216 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6282 (pttp) REVERT: B 262 MET cc_start: 0.3711 (pmm) cc_final: 0.3257 (ptt) REVERT: N 109 ASP cc_start: 0.4837 (m-30) cc_final: 0.4582 (m-30) REVERT: R 221 GLN cc_start: 0.8897 (mm110) cc_final: 0.8254 (tm-30) REVERT: R 269 TYR cc_start: 0.7667 (m-80) cc_final: 0.7302 (m-80) REVERT: R 393 PHE cc_start: 0.8519 (m-80) cc_final: 0.8147 (m-80) outliers start: 36 outliers final: 31 residues processed: 146 average time/residue: 0.1708 time to fit residues: 36.3962 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.0030 chunk 63 optimal weight: 20.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 230 ASN N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.094460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.073630 restraints weight = 42385.217| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 7.42 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9434 Z= 0.181 Angle : 0.734 10.461 12823 Z= 0.359 Chirality : 0.046 0.283 1426 Planarity : 0.004 0.035 1593 Dihedral : 5.917 50.886 1627 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.48 % Allowed : 25.72 % Favored : 70.80 % 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: 0.26 (0.26), residues: 1104 helix: 1.27 (0.26), residues: 429 sheet: -0.13 (0.36), residues: 209 loop : -0.65 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP N 36 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE R 280 TYR 0.022 0.002 TYR N 94 ARG 0.009 0.001 ARG N 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.03 seconds wall clock time: 43 minutes 35.54 seconds (2615.54 seconds total)