Starting phenix.real_space_refine on Thu Feb 13 00:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d68_30590/02_2025/7d68_30590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d68_30590/02_2025/7d68_30590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d68_30590/02_2025/7d68_30590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d68_30590/02_2025/7d68_30590.map" model { file = "/net/cci-nas-00/data/ceres_data/7d68_30590/02_2025/7d68_30590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d68_30590/02_2025/7d68_30590.cif" } resolution = 3.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5447 2.51 5 N 1496 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8564 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1885 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 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: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "R" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2426 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 8, 'TRANS': 283} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 4.85, per 1000 atoms: 0.57 Number of scatterers: 8564 At special positions: 0 Unit cell: (104.442, 95.316, 137.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1571 8.00 N 1496 7.00 C 5447 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 330 " distance=2.04 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.978A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.764A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.792A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.922A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.753A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.685A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.990A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.616A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.718A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.533A pdb=" N PHE P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 203 removed outlier: 3.844A pdb=" N ASP R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 239 Processing helix chain 'R' and resid 252 through 257 removed outlier: 3.567A pdb=" N GLU R 255 " --> pdb=" O TYR R 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET R 256 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER R 257 " --> pdb=" O SER R 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 252 through 257' Processing helix chain 'R' and resid 258 through 288 removed outlier: 3.697A pdb=" N SER R 262 " --> pdb=" O THR R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 308 Processing helix chain 'R' and resid 311 through 325 Proline residue: R 317 - end of helix removed outlier: 3.855A pdb=" N ALA R 323 " --> pdb=" O GLY R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 371 Proline residue: R 346 - end of helix removed outlier: 4.074A pdb=" N CYS R 350 " --> pdb=" O PRO R 346 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN R 354 " --> pdb=" O CYS R 350 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA R 371 " --> pdb=" O SER R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 395 Proline residue: R 392 - end of helix Processing helix chain 'R' and resid 398 through 404 removed outlier: 3.557A pdb=" N PHE R 403 " --> pdb=" O ILE R 399 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE R 404 " --> pdb=" O LEU R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 411 through 437 removed outlier: 3.559A pdb=" N LEU R 415 " --> pdb=" O GLY R 411 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY R 429 " --> pdb=" O SER R 425 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE R 430 " --> pdb=" O SER R 426 " (cutoff:3.500A) Processing helix chain 'R' and resid 440 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.608A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.733A 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 52 removed outlier: 3.592A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.901A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.957A 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: 6.989A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.638A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.939A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.483A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.684A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.516A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.616A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1152 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: 2.50 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2187 1.33 - 1.45: 1828 1.45 - 1.58: 4652 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8739 Sorted by residual: bond pdb=" C ARG R 210 " pdb=" O ARG R 210 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.48e+00 bond pdb=" C LEU R 206 " pdb=" O LEU R 206 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.32e-02 5.74e+03 4.11e+00 bond pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.12e-02 7.97e+03 2.35e+00 bond pdb=" C TYR A 358 " pdb=" O TYR A 358 " ideal model delta sigma weight residual 1.234 1.215 0.018 1.22e-02 6.72e+03 2.29e+00 bond pdb=" C HIS A 357 " pdb=" O HIS A 357 " ideal model delta sigma weight residual 1.234 1.216 0.017 1.24e-02 6.50e+03 1.99e+00 ... (remaining 8734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 11632 2.12 - 4.24: 169 4.24 - 6.36: 18 6.36 - 8.48: 5 8.48 - 10.60: 1 Bond angle restraints: 11825 Sorted by residual: angle pdb=" N ARG A 356 " pdb=" CA ARG A 356 " pdb=" C ARG A 356 " ideal model delta sigma weight residual 113.88 105.69 8.19 1.23e+00 6.61e-01 4.43e+01 angle pdb=" N HIS R 207 " pdb=" CA HIS R 207 " pdb=" C HIS R 207 " ideal model delta sigma weight residual 110.80 121.40 -10.60 2.13e+00 2.20e-01 2.48e+01 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 112.04 106.17 5.87 1.44e+00 4.82e-01 1.66e+01 angle pdb=" N GLU R 442 " pdb=" CA GLU R 442 " pdb=" C GLU R 442 " ideal model delta sigma weight residual 111.28 115.36 -4.08 1.09e+00 8.42e-01 1.40e+01 angle pdb=" N SER R 402 " pdb=" CA SER R 402 " pdb=" C SER R 402 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 ... (remaining 11820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4680 16.16 - 32.32: 401 32.32 - 48.48: 84 48.48 - 64.64: 17 64.64 - 80.80: 6 Dihedral angle restraints: 5188 sinusoidal: 2077 harmonic: 3111 Sorted by residual: dihedral pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " pdb=" SG CYS R 330 " pdb=" CB CYS R 330 " ideal model delta sinusoidal sigma weight residual 93.00 40.15 52.85 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LYS A 216 " pdb=" C LYS A 216 " pdb=" N VAL A 217 " pdb=" CA VAL A 217 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1205 0.080 - 0.159: 109 0.159 - 0.239: 2 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA HIS R 207 " pdb=" N HIS R 207 " pdb=" C HIS R 207 " pdb=" CB HIS R 207 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA ASP A 354 " pdb=" N ASP A 354 " pdb=" C ASP A 354 " pdb=" CB ASP A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE R 404 " pdb=" N ILE R 404 " pdb=" C ILE R 404 " pdb=" CB ILE R 404 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1314 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 345 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO R 346 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 346 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 346 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.014 2.00e-02 2.50e+03 1.37e-02 3.74e+00 pdb=" CG TYR B 59 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 350 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C THR A 350 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 350 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 351 " -0.010 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 137 2.68 - 3.23: 8179 3.23 - 3.79: 12857 3.79 - 4.34: 17957 4.34 - 4.90: 30124 Nonbonded interactions: 69254 Sorted by model distance: nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.121 3.040 nonbonded pdb=" NH1 ARG B 22 " pdb=" O ALA B 257 " model vdw 2.210 3.120 nonbonded pdb=" ND2 ASN N 35 " pdb=" OD2 ASP N 109 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.238 3.120 nonbonded pdb=" OE1 GLU R 281 " pdb=" O HOH R 701 " model vdw 2.244 3.040 ... (remaining 69249 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: 0.640 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.500 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.004 0.043 8739 Z= 0.263 Angle : 0.664 10.598 11825 Z= 0.395 Chirality : 0.045 0.398 1317 Planarity : 0.004 0.050 1503 Dihedral : 13.068 80.805 3170 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 0.76 % Allowed : 3.89 % Favored : 95.36 % 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: -2.09 (0.23), residues: 1052 helix: -0.47 (0.23), residues: 390 sheet: -1.37 (0.32), residues: 220 loop : -2.17 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.007 0.001 HIS B 62 PHE 0.015 0.002 PHE A 222 TYR 0.034 0.002 TYR B 59 ARG 0.006 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 341 ILE cc_start: 0.7881 (mm) cc_final: 0.7526 (mm) REVERT: A 373 ARG cc_start: 0.7304 (mmm160) cc_final: 0.7072 (mmt180) REVERT: R 215 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7586 (mtp) REVERT: R 338 LYS cc_start: 0.7552 (mttm) cc_final: 0.6846 (tttp) outliers start: 7 outliers final: 2 residues processed: 157 average time/residue: 1.3750 time to fit residues: 228.6328 Evaluate side-chains 124 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain R residue 215 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 371 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN N 77 ASN ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 372 HIS R 408 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148444 restraints weight = 9485.654| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.15 r_work: 0.3477 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8739 Z= 0.227 Angle : 0.601 7.419 11825 Z= 0.316 Chirality : 0.043 0.164 1317 Planarity : 0.004 0.052 1503 Dihedral : 4.960 31.739 1176 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.62 % Allowed : 12.10 % Favored : 86.29 % 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: -0.96 (0.25), residues: 1052 helix: 0.68 (0.25), residues: 412 sheet: -0.82 (0.33), residues: 212 loop : -1.82 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.005 0.001 HIS B 62 PHE 0.020 0.002 PHE R 202 TYR 0.028 0.001 TYR R 182 ARG 0.005 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6771 (tm-30) cc_final: 0.6368 (tm-30) REVERT: A 268 GLU cc_start: 0.7693 (mp0) cc_final: 0.7314 (mp0) REVERT: A 322 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 341 ILE cc_start: 0.7802 (mm) cc_final: 0.7575 (mm) REVERT: B 145 TYR cc_start: 0.9058 (p90) cc_final: 0.8838 (p90) REVERT: B 270 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7608 (pp) REVERT: B 290 ASP cc_start: 0.7805 (m-30) cc_final: 0.7487 (m-30) REVERT: N 80 TYR cc_start: 0.7683 (m-10) cc_final: 0.7375 (m-80) REVERT: N 83 MET cc_start: 0.6858 (mtm) cc_final: 0.6513 (mtp) REVERT: R 255 GLU cc_start: 0.7083 (mp0) cc_final: 0.6857 (mp0) REVERT: R 326 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: R 338 LYS cc_start: 0.7773 (mttm) cc_final: 0.6734 (tttp) outliers start: 15 outliers final: 4 residues processed: 133 average time/residue: 1.2975 time to fit residues: 183.7339 Evaluate side-chains 124 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 326 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 35 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147873 restraints weight = 9675.242| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.20 r_work: 0.3502 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8739 Z= 0.258 Angle : 0.589 6.989 11825 Z= 0.310 Chirality : 0.043 0.169 1317 Planarity : 0.004 0.058 1503 Dihedral : 4.620 21.562 1170 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.16 % Allowed : 15.44 % Favored : 82.40 % 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: -0.61 (0.25), residues: 1052 helix: 1.01 (0.25), residues: 412 sheet: -0.64 (0.33), residues: 212 loop : -1.68 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS B 62 PHE 0.021 0.002 PHE R 202 TYR 0.027 0.001 TYR R 182 ARG 0.006 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.905 Fit side-chains REVERT: A 31 GLN cc_start: 0.6975 (tp40) cc_final: 0.6755 (tp-100) REVERT: A 268 GLU cc_start: 0.7801 (mp0) cc_final: 0.7342 (mp0) REVERT: A 341 ILE cc_start: 0.7853 (mm) cc_final: 0.7587 (mm) REVERT: B 59 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: B 145 TYR cc_start: 0.9111 (p90) cc_final: 0.8903 (p90) REVERT: B 198 LEU cc_start: 0.8946 (mt) cc_final: 0.8703 (mt) REVERT: B 262 MET cc_start: 0.7868 (mpp) cc_final: 0.7311 (mpt) REVERT: B 270 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7670 (pp) REVERT: B 290 ASP cc_start: 0.7814 (m-30) cc_final: 0.7487 (m-30) REVERT: N 20 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7326 (mm) REVERT: N 80 TYR cc_start: 0.7668 (m-10) cc_final: 0.7378 (m-80) REVERT: R 326 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: R 338 LYS cc_start: 0.7818 (mttm) cc_final: 0.6780 (tttp) REVERT: R 412 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5175 (t80) outliers start: 20 outliers final: 6 residues processed: 125 average time/residue: 1.2432 time to fit residues: 165.7976 Evaluate side-chains 124 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 412 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.149871 restraints weight = 9563.486| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.19 r_work: 0.3509 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8739 Z= 0.182 Angle : 0.536 7.821 11825 Z= 0.282 Chirality : 0.041 0.154 1317 Planarity : 0.004 0.060 1503 Dihedral : 4.374 21.630 1170 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.48 % Allowed : 16.41 % 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: -0.27 (0.26), residues: 1052 helix: 1.40 (0.26), residues: 413 sheet: -0.55 (0.34), residues: 211 loop : -1.57 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.002 0.001 HIS P 1 PHE 0.023 0.001 PHE R 202 TYR 0.022 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.908 Fit side-chains REVERT: A 211 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7752 (pttm) REVERT: A 341 ILE cc_start: 0.7778 (mm) cc_final: 0.7518 (mm) REVERT: B 59 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: B 61 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8696 (ppp) REVERT: B 145 TYR cc_start: 0.9066 (p90) cc_final: 0.8805 (p90) REVERT: B 220 GLN cc_start: 0.8045 (mt0) cc_final: 0.7531 (mt0) REVERT: B 262 MET cc_start: 0.7841 (mpp) cc_final: 0.7193 (mpt) REVERT: B 270 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7650 (pp) REVERT: B 290 ASP cc_start: 0.7693 (m-30) cc_final: 0.7388 (m-30) REVERT: N 20 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7290 (mm) REVERT: N 68 PHE cc_start: 0.6991 (m-10) cc_final: 0.6786 (m-10) REVERT: N 80 TYR cc_start: 0.7598 (m-10) cc_final: 0.7281 (m-80) REVERT: R 255 GLU cc_start: 0.7039 (mp0) cc_final: 0.6817 (mp0) REVERT: R 302 ARG cc_start: 0.6833 (mtp180) cc_final: 0.6069 (mmt-90) REVERT: R 326 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.5637 (mp0) REVERT: R 338 LYS cc_start: 0.7863 (mttm) cc_final: 0.6740 (tttp) REVERT: R 412 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5014 (t80) outliers start: 23 outliers final: 10 residues processed: 132 average time/residue: 1.2406 time to fit residues: 174.7004 Evaluate side-chains 135 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 412 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 40.0000 chunk 79 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 239 ASN ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.191309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150754 restraints weight = 9638.264| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.25 r_work: 0.3630 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8739 Z= 0.184 Angle : 0.532 7.763 11825 Z= 0.279 Chirality : 0.041 0.152 1317 Planarity : 0.004 0.059 1503 Dihedral : 4.269 20.436 1170 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.59 % Allowed : 17.49 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.26), residues: 1052 helix: 1.41 (0.26), residues: 420 sheet: -0.47 (0.34), residues: 211 loop : -1.48 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS R 428 PHE 0.023 0.001 PHE R 202 TYR 0.023 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.771 Fit side-chains REVERT: A 211 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7810 (pttm) REVERT: A 341 ILE cc_start: 0.7880 (mm) cc_final: 0.7614 (mm) REVERT: B 59 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: B 61 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8647 (ppp) REVERT: B 145 TYR cc_start: 0.9128 (p90) cc_final: 0.8882 (p90) REVERT: B 262 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7289 (mpt) REVERT: B 270 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7700 (pp) REVERT: B 290 ASP cc_start: 0.7793 (m-30) cc_final: 0.7486 (m-30) REVERT: N 20 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7424 (mm) REVERT: N 68 PHE cc_start: 0.6986 (m-10) cc_final: 0.6694 (m-80) REVERT: N 80 TYR cc_start: 0.7447 (m-10) cc_final: 0.7229 (m-80) REVERT: R 255 GLU cc_start: 0.7138 (mp0) cc_final: 0.6891 (mp0) REVERT: R 302 ARG cc_start: 0.6928 (mtp180) cc_final: 0.6192 (mmt-90) REVERT: R 326 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.5729 (mp0) REVERT: R 338 LYS cc_start: 0.7958 (mttm) cc_final: 0.6878 (tttp) REVERT: R 348 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6219 (ttt) REVERT: R 412 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.4880 (t80) outliers start: 24 outliers final: 11 residues processed: 123 average time/residue: 1.2627 time to fit residues: 165.4221 Evaluate side-chains 138 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 348 MET Chi-restraints excluded: chain R residue 412 PHE Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 239 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152058 restraints weight = 9499.137| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.22 r_work: 0.3642 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8739 Z= 0.170 Angle : 0.513 7.201 11825 Z= 0.271 Chirality : 0.040 0.151 1317 Planarity : 0.004 0.058 1503 Dihedral : 4.154 19.836 1170 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.24 % Allowed : 17.60 % Favored : 79.16 % 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: 0.00 (0.26), residues: 1052 helix: 1.54 (0.26), residues: 419 sheet: -0.31 (0.35), residues: 208 loop : -1.41 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS R 428 PHE 0.027 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.926 Fit side-chains REVERT: A 211 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7828 (pttm) REVERT: A 268 GLU cc_start: 0.7611 (mp0) cc_final: 0.7318 (mm-30) REVERT: A 341 ILE cc_start: 0.7839 (mm) cc_final: 0.7575 (mm) REVERT: B 59 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: B 61 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8637 (ppp) REVERT: B 134 ARG cc_start: 0.7431 (ptp-110) cc_final: 0.6993 (ptp-170) REVERT: B 262 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7325 (mpt) REVERT: B 270 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7720 (pp) REVERT: B 290 ASP cc_start: 0.7739 (m-30) cc_final: 0.7498 (m-30) REVERT: G 47 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5715 (mp0) REVERT: N 20 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7535 (mm) REVERT: N 68 PHE cc_start: 0.6813 (m-10) cc_final: 0.6549 (m-80) REVERT: N 80 TYR cc_start: 0.7396 (m-10) cc_final: 0.7163 (m-80) REVERT: R 188 PHE cc_start: 0.7516 (m-10) cc_final: 0.7026 (t80) REVERT: R 302 ARG cc_start: 0.6887 (mtp180) cc_final: 0.6183 (mmt-90) REVERT: R 326 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: R 338 LYS cc_start: 0.7930 (mttm) cc_final: 0.6887 (tttp) outliers start: 30 outliers final: 14 residues processed: 131 average time/residue: 1.2503 time to fit residues: 174.4261 Evaluate side-chains 137 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 0.0030 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 92 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 84 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.195013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155392 restraints weight = 9557.926| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.18 r_work: 0.3681 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8739 Z= 0.133 Angle : 0.497 6.459 11825 Z= 0.261 Chirality : 0.039 0.148 1317 Planarity : 0.004 0.056 1503 Dihedral : 3.927 18.744 1170 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.48 % Allowed : 19.01 % Favored : 78.51 % 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: 0.35 (0.26), residues: 1052 helix: 1.88 (0.27), residues: 410 sheet: 0.24 (0.37), residues: 190 loop : -1.37 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS R 428 PHE 0.029 0.001 PHE R 202 TYR 0.018 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.983 Fit side-chains REVERT: A 211 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7553 (mmmt) REVERT: A 268 GLU cc_start: 0.7614 (mp0) cc_final: 0.7315 (mm-30) REVERT: A 341 ILE cc_start: 0.7796 (mm) cc_final: 0.7516 (mm) REVERT: B 59 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: B 61 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (ppp) REVERT: B 134 ARG cc_start: 0.7404 (ptp-110) cc_final: 0.7009 (ptp-170) REVERT: B 262 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7216 (mpt) REVERT: B 270 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7706 (pp) REVERT: B 290 ASP cc_start: 0.7689 (m-30) cc_final: 0.7418 (m-30) REVERT: G 47 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5596 (mp0) REVERT: N 80 TYR cc_start: 0.7240 (m-10) cc_final: 0.6992 (m-80) REVERT: R 188 PHE cc_start: 0.7564 (m-10) cc_final: 0.7040 (t80) REVERT: R 326 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.5644 (mp0) REVERT: R 338 LYS cc_start: 0.7949 (mttm) cc_final: 0.6944 (tttp) outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 1.2370 time to fit residues: 174.6223 Evaluate side-chains 134 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 75 GLN B 239 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152535 restraints weight = 9623.843| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.23 r_work: 0.3624 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8739 Z= 0.179 Angle : 0.513 6.532 11825 Z= 0.269 Chirality : 0.040 0.150 1317 Planarity : 0.004 0.054 1503 Dihedral : 3.971 18.065 1170 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.02 % Allowed : 19.22 % Favored : 77.75 % 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: 0.34 (0.26), residues: 1052 helix: 1.87 (0.26), residues: 409 sheet: 0.20 (0.37), residues: 190 loop : -1.35 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 277 HIS 0.003 0.001 HIS R 428 PHE 0.027 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.914 Fit side-chains REVERT: A 31 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6184 (tp-100) REVERT: A 211 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7525 (mmmt) REVERT: A 268 GLU cc_start: 0.7690 (mp0) cc_final: 0.7355 (mm-30) REVERT: A 341 ILE cc_start: 0.7821 (mm) cc_final: 0.7514 (mm) REVERT: B 59 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: B 61 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8539 (pp-130) REVERT: B 134 ARG cc_start: 0.7395 (ptp-110) cc_final: 0.6991 (ptp-170) REVERT: B 262 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7225 (mpt) REVERT: B 270 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7733 (pp) REVERT: B 290 ASP cc_start: 0.7666 (m-30) cc_final: 0.7456 (m-30) REVERT: G 47 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5523 (mp0) REVERT: N 83 MET cc_start: 0.6771 (mtm) cc_final: 0.6504 (mtp) REVERT: R 188 PHE cc_start: 0.7557 (m-10) cc_final: 0.7004 (t80) REVERT: R 255 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7043 (mp0) REVERT: R 302 ARG cc_start: 0.6896 (mtp-110) cc_final: 0.6258 (mmt-90) REVERT: R 326 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.5727 (mp0) REVERT: R 338 LYS cc_start: 0.7952 (mttm) cc_final: 0.6951 (tttp) outliers start: 28 outliers final: 12 residues processed: 131 average time/residue: 1.2671 time to fit residues: 176.9385 Evaluate side-chains 135 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.193991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154407 restraints weight = 9641.820| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.20 r_work: 0.3658 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8739 Z= 0.157 Angle : 0.511 6.389 11825 Z= 0.267 Chirality : 0.041 0.234 1317 Planarity : 0.004 0.057 1503 Dihedral : 3.966 22.647 1170 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.02 % Allowed : 19.44 % Favored : 77.54 % 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: 0.37 (0.26), residues: 1052 helix: 1.82 (0.26), residues: 415 sheet: 0.24 (0.36), residues: 190 loop : -1.31 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS R 428 PHE 0.029 0.001 PHE R 202 TYR 0.019 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.968 Fit side-chains REVERT: A 31 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6218 (tp-100) REVERT: A 211 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7741 (pttm) REVERT: A 220 HIS cc_start: 0.8051 (m-70) cc_final: 0.7814 (t-90) REVERT: A 268 GLU cc_start: 0.7660 (mp0) cc_final: 0.7333 (mm-30) REVERT: A 341 ILE cc_start: 0.7799 (mm) cc_final: 0.7494 (mm) REVERT: A 370 GLU cc_start: 0.7158 (tt0) cc_final: 0.6911 (tp30) REVERT: B 59 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: B 61 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8525 (pp-130) REVERT: B 134 ARG cc_start: 0.7385 (ptp-110) cc_final: 0.6989 (ptp-170) REVERT: B 262 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7099 (mpt) REVERT: B 270 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7736 (pp) REVERT: G 47 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5452 (mp0) REVERT: N 80 TYR cc_start: 0.7360 (m-80) cc_final: 0.6946 (m-80) REVERT: R 188 PHE cc_start: 0.7551 (m-10) cc_final: 0.7001 (t80) REVERT: R 255 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7198 (mp0) REVERT: R 326 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.5735 (mp0) REVERT: R 338 LYS cc_start: 0.7957 (mttm) cc_final: 0.6986 (tttp) outliers start: 28 outliers final: 14 residues processed: 132 average time/residue: 1.2358 time to fit residues: 173.8835 Evaluate side-chains 133 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 0.0030 chunk 11 optimal weight: 0.0970 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 239 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.194634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154677 restraints weight = 9557.055| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.20 r_work: 0.3674 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8739 Z= 0.146 Angle : 0.498 6.448 11825 Z= 0.262 Chirality : 0.040 0.145 1317 Planarity : 0.004 0.056 1503 Dihedral : 3.887 23.575 1170 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.81 % Allowed : 19.76 % Favored : 77.43 % 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: 0.45 (0.26), residues: 1052 helix: 1.88 (0.26), residues: 416 sheet: 0.36 (0.37), residues: 190 loop : -1.30 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 340 HIS 0.003 0.001 HIS R 428 PHE 0.032 0.001 PHE R 202 TYR 0.019 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.980 Fit side-chains REVERT: A 31 GLN cc_start: 0.6849 (mm-40) cc_final: 0.6202 (tp-100) REVERT: A 211 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7794 (pttm) REVERT: A 268 GLU cc_start: 0.7636 (mp0) cc_final: 0.7353 (mm-30) REVERT: A 341 ILE cc_start: 0.7734 (mm) cc_final: 0.7431 (mm) REVERT: A 370 GLU cc_start: 0.7143 (tt0) cc_final: 0.6896 (tp30) REVERT: B 59 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: B 61 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8508 (pp-130) REVERT: B 134 ARG cc_start: 0.7376 (ptp-110) cc_final: 0.6996 (ptp-170) REVERT: B 270 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7735 (pp) REVERT: G 47 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5352 (mp0) REVERT: N 68 PHE cc_start: 0.6400 (m-10) cc_final: 0.5988 (m-80) REVERT: N 80 TYR cc_start: 0.7185 (m-80) cc_final: 0.6795 (m-80) REVERT: P 28 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6598 (mp-120) REVERT: R 188 PHE cc_start: 0.7539 (m-10) cc_final: 0.6999 (t80) REVERT: R 255 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7205 (mp0) REVERT: R 326 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.5667 (mp0) REVERT: R 338 LYS cc_start: 0.7891 (mttm) cc_final: 0.6976 (tttp) outliers start: 26 outliers final: 12 residues processed: 132 average time/residue: 1.2188 time to fit residues: 171.5389 Evaluate side-chains 133 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 15 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 239 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.195907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155964 restraints weight = 9594.407| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.20 r_work: 0.3688 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8739 Z= 0.132 Angle : 0.489 6.565 11825 Z= 0.258 Chirality : 0.039 0.143 1317 Planarity : 0.004 0.056 1503 Dihedral : 3.854 23.147 1170 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.16 % Allowed : 20.52 % Favored : 77.32 % 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: 0.57 (0.26), residues: 1052 helix: 1.94 (0.26), residues: 416 sheet: 0.49 (0.37), residues: 190 loop : -1.22 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 340 HIS 0.003 0.001 HIS A 220 PHE 0.035 0.001 PHE R 202 TYR 0.018 0.001 TYR R 182 ARG 0.002 0.000 ARG R 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6820.61 seconds wall clock time: 121 minutes 4.44 seconds (7264.44 seconds total)