Starting phenix.real_space_refine on Sat Jul 26 10:05:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d68_30590/07_2025/7d68_30590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d68_30590/07_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_30590/07_2025/7d68_30590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d68_30590/07_2025/7d68_30590.map" model { file = "/net/cci-nas-00/data/ceres_data/7d68_30590/07_2025/7d68_30590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d68_30590/07_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-5711/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: 4.95, per 1000 atoms: 0.58 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: 2.00 Conformation dependent library (CDL) restraints added in 946.4 milliseconds 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: 0.85 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: 2.51 Time building geometry restraints manager: 2.42 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: 0.460 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- 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 8741 Z= 0.193 Angle : 0.664 10.598 11829 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 Details of bonding type rmsd hydrogen bonds : bond 0.16442 ( 400) hydrogen bonds : angle 6.35834 ( 1152) SS BOND : bond 0.00410 ( 2) SS BOND : angle 1.64694 ( 4) covalent geometry : bond 0.00397 ( 8739) covalent geometry : angle 0.66377 (11825) *********************** 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 : 0.987 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: 1.3018 time to fit residues: 216.7895 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 : 0.991 ------------------------------------------------------------------------------- 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 = 57)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148446 restraints weight = 9485.662| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.15 r_work: 0.3476 rms_B_bonded: 2.87 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 8741 Z= 0.153 Angle : 0.602 7.419 11829 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 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 400) hydrogen bonds : angle 4.83521 ( 1152) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.32748 ( 4) covalent geometry : bond 0.00345 ( 8739) covalent geometry : angle 0.60122 (11825) *********************** 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 : 0.856 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6370 (tm-30) REVERT: A 268 GLU cc_start: 0.7692 (mp0) cc_final: 0.7314 (mp0) REVERT: A 322 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6853 (mm-30) REVERT: A 341 ILE cc_start: 0.7801 (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: 0.8133 (OUTLIER) cc_final: 0.7605 (pp) REVERT: B 290 ASP cc_start: 0.7804 (m-30) cc_final: 0.7487 (m-30) REVERT: N 80 TYR cc_start: 0.7685 (m-10) cc_final: 0.7378 (m-80) REVERT: N 83 MET cc_start: 0.6861 (mtm) cc_final: 0.6516 (mtp) REVERT: R 255 GLU cc_start: 0.7081 (mp0) cc_final: 0.6855 (mp0) REVERT: R 326 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5601 (mp0) REVERT: R 338 LYS cc_start: 0.7775 (mttm) cc_final: 0.6736 (tttp) outliers start: 15 outliers final: 4 residues processed: 133 average time/residue: 1.2615 time to fit residues: 178.5322 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 : 0.962 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150528 restraints weight = 9636.356| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.20 r_work: 0.3506 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8741 Z= 0.126 Angle : 0.548 6.351 11829 Z= 0.290 Chirality : 0.041 0.167 1317 Planarity : 0.004 0.056 1503 Dihedral : 4.476 21.479 1170 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.84 % Allowed : 15.33 % Favored : 82.83 % 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 (0.25), residues: 1052 helix: 1.13 (0.26), residues: 418 sheet: -0.58 (0.34), residues: 211 loop : -1.59 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS P 1 PHE 0.022 0.001 PHE R 202 TYR 0.024 0.001 TYR R 182 ARG 0.006 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 400) hydrogen bonds : angle 4.44612 ( 1152) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.01539 ( 4) covalent geometry : bond 0.00277 ( 8739) covalent geometry : angle 0.54827 (11825) *********************** 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 138 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6999 (tp40) cc_final: 0.6782 (tp-100) REVERT: A 341 ILE cc_start: 0.7800 (mm) cc_final: 0.7571 (mm) REVERT: B 59 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: B 145 TYR cc_start: 0.9070 (p90) cc_final: 0.8812 (p90) REVERT: B 198 LEU cc_start: 0.8850 (mt) cc_final: 0.8642 (mt) REVERT: B 262 MET cc_start: 0.7742 (mpp) cc_final: 0.7194 (mpt) REVERT: B 270 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7611 (pp) REVERT: B 290 ASP cc_start: 0.7744 (m-30) cc_final: 0.7466 (m-30) REVERT: G 38 MET cc_start: 0.4650 (tmm) cc_final: 0.4004 (tpt) REVERT: N 80 TYR cc_start: 0.7604 (m-10) cc_final: 0.7246 (m-80) REVERT: N 83 MET cc_start: 0.6925 (mtm) cc_final: 0.6691 (mtp) REVERT: R 255 GLU cc_start: 0.7149 (mp0) cc_final: 0.6910 (mp0) REVERT: R 326 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: R 338 LYS cc_start: 0.7793 (mttm) cc_final: 0.6740 (tttp) REVERT: R 412 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5074 (t80) outliers start: 17 outliers final: 4 residues processed: 125 average time/residue: 1.2395 time to fit residues: 165.1569 Evaluate side-chains 126 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.0270 chunk 66 optimal weight: 0.0060 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5054 ------------------------------------------------------------------------------- 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 ** 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 = 0.4191 r_free = 0.4191 target = 0.192307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152385 restraints weight = 9493.095| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.18 r_work: 0.3557 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8741 Z= 0.108 Angle : 0.509 6.656 11829 Z= 0.269 Chirality : 0.040 0.155 1317 Planarity : 0.004 0.054 1503 Dihedral : 4.217 21.117 1170 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.38 % Allowed : 15.87 % Favored : 81.75 % 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: -0.08 (0.26), residues: 1052 helix: 1.56 (0.26), residues: 414 sheet: -0.45 (0.34), residues: 211 loop : -1.46 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS R 428 PHE 0.024 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 400) hydrogen bonds : angle 4.16593 ( 1152) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.91080 ( 4) covalent geometry : bond 0.00229 ( 8739) covalent geometry : angle 0.50863 (11825) *********************** 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 148 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.931 Fit side-chains REVERT: A 12 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6696 (tm-30) REVERT: A 31 GLN cc_start: 0.6897 (tp-100) cc_final: 0.6636 (tp-100) REVERT: A 211 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7715 (pttm) REVERT: A 341 ILE cc_start: 0.7732 (mm) cc_final: 0.7496 (mm) REVERT: B 59 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: B 61 MET cc_start: 0.8992 (pp-130) cc_final: 0.8707 (ppp) REVERT: B 145 TYR cc_start: 0.9055 (p90) cc_final: 0.8815 (p90) REVERT: B 262 MET cc_start: 0.7659 (mpp) cc_final: 0.7019 (mpt) REVERT: B 270 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7623 (pp) REVERT: B 290 ASP cc_start: 0.7661 (m-30) cc_final: 0.7360 (m-30) REVERT: N 68 PHE cc_start: 0.7002 (m-10) cc_final: 0.6769 (m-10) REVERT: N 80 TYR cc_start: 0.7439 (m-10) cc_final: 0.7153 (m-80) REVERT: R 188 PHE cc_start: 0.7383 (m-10) cc_final: 0.6921 (t80) REVERT: R 302 ARG cc_start: 0.6842 (mtp180) cc_final: 0.6088 (mmt-90) REVERT: R 326 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.5576 (mp0) REVERT: R 338 LYS cc_start: 0.7871 (mttm) cc_final: 0.6768 (tttp) REVERT: R 412 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5002 (t80) outliers start: 22 outliers final: 9 residues processed: 137 average time/residue: 1.2062 time to fit residues: 176.0752 Evaluate side-chains 133 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR 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 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: 3.9990 chunk 80 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 51 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.193279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153023 restraints weight = 9573.892| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.22 r_work: 0.3572 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8741 Z= 0.113 Angle : 0.513 6.314 11829 Z= 0.270 Chirality : 0.040 0.153 1317 Planarity : 0.004 0.055 1503 Dihedral : 4.124 19.980 1170 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.70 % Allowed : 17.60 % Favored : 79.70 % 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: 0.02 (0.26), residues: 1052 helix: 1.55 (0.26), residues: 420 sheet: -0.34 (0.34), residues: 211 loop : -1.37 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 220 PHE 0.025 0.001 PHE R 202 TYR 0.022 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 400) hydrogen bonds : angle 4.06787 ( 1152) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.85769 ( 4) covalent geometry : bond 0.00248 ( 8739) covalent geometry : angle 0.51234 (11825) *********************** 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: 25 poor density : 114 time to evaluate : 0.892 Fit side-chains REVERT: A 211 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7815 (pttm) REVERT: A 341 ILE cc_start: 0.7779 (mm) cc_final: 0.7517 (mm) REVERT: B 59 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: B 61 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8658 (ppp) REVERT: B 134 ARG cc_start: 0.7373 (ptp-110) cc_final: 0.6931 (ptp-170) REVERT: B 262 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7115 (mpt) REVERT: B 270 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7683 (pp) REVERT: B 290 ASP cc_start: 0.7685 (m-30) cc_final: 0.7452 (m-30) REVERT: N 68 PHE cc_start: 0.6985 (m-10) cc_final: 0.6586 (m-80) REVERT: N 80 TYR cc_start: 0.7356 (m-10) cc_final: 0.7114 (m-80) REVERT: R 188 PHE cc_start: 0.7537 (m-10) cc_final: 0.6995 (t80) REVERT: R 302 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6166 (mmt-90) REVERT: R 326 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.5622 (mp0) REVERT: R 338 LYS cc_start: 0.7909 (mttm) cc_final: 0.6862 (tttp) REVERT: R 412 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.4871 (t80) outliers start: 25 outliers final: 13 residues processed: 124 average time/residue: 1.2029 time to fit residues: 159.1970 Evaluate side-chains 133 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 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 37 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 313 LEU Chi-restraints excluded: chain R residue 326 GLU 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: 0.9990 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.0010 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN 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 = 0.4170 r_free = 0.4170 target = 0.191282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150739 restraints weight = 9545.115| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.26 r_work: 0.3545 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8741 Z= 0.110 Angle : 0.503 6.149 11829 Z= 0.265 Chirality : 0.040 0.152 1317 Planarity : 0.004 0.054 1503 Dihedral : 4.025 18.893 1170 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.35 % Allowed : 17.60 % Favored : 79.05 % 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: 0.17 (0.26), residues: 1052 helix: 1.65 (0.26), residues: 420 sheet: 0.03 (0.36), residues: 196 loop : -1.41 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS R 428 PHE 0.024 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 400) hydrogen bonds : angle 3.98282 ( 1152) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.84010 ( 4) covalent geometry : bond 0.00241 ( 8739) covalent geometry : angle 0.50240 (11825) *********************** 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 147 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.922 Fit side-chains REVERT: A 211 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7760 (pttm) REVERT: A 220 HIS cc_start: 0.7958 (m-70) cc_final: 0.7631 (t-90) REVERT: A 341 ILE cc_start: 0.7748 (mm) cc_final: 0.7479 (mm) REVERT: B 59 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: B 61 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8651 (ppp) REVERT: B 75 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8995 (tp40) REVERT: B 134 ARG cc_start: 0.7336 (ptp-110) cc_final: 0.6903 (ptp-170) REVERT: B 262 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7148 (mpt) REVERT: B 270 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7677 (pp) REVERT: B 290 ASP cc_start: 0.7618 (m-30) cc_final: 0.7389 (m-30) REVERT: N 68 PHE cc_start: 0.6745 (m-10) cc_final: 0.6470 (m-80) REVERT: N 80 TYR cc_start: 0.7277 (m-10) cc_final: 0.7007 (m-80) REVERT: R 188 PHE cc_start: 0.7433 (m-10) cc_final: 0.6908 (t80) REVERT: R 302 ARG cc_start: 0.6828 (mtp180) cc_final: 0.6090 (mmt-90) REVERT: R 326 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5633 (mp0) REVERT: R 338 LYS cc_start: 0.7889 (mttm) cc_final: 0.6887 (tttp) outliers start: 31 outliers final: 13 residues processed: 130 average time/residue: 1.9820 time to fit residues: 278.2081 Evaluate side-chains 133 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 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 75 GLN 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 37 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 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 92 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.193426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152855 restraints weight = 9692.588| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.25 r_work: 0.3598 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8741 Z= 0.111 Angle : 0.505 5.939 11829 Z= 0.266 Chirality : 0.040 0.151 1317 Planarity : 0.004 0.055 1503 Dihedral : 3.997 18.404 1170 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.13 % Allowed : 18.90 % Favored : 77.97 % 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: 0.25 (0.26), residues: 1052 helix: 1.72 (0.26), residues: 416 sheet: 0.09 (0.36), residues: 195 loop : -1.35 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS R 428 PHE 0.025 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 400) hydrogen bonds : angle 3.94653 ( 1152) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.79496 ( 4) covalent geometry : bond 0.00244 ( 8739) covalent geometry : angle 0.50519 (11825) *********************** 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 143 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.949 Fit side-chains REVERT: A 211 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7794 (pttm) REVERT: A 341 ILE cc_start: 0.7808 (mm) cc_final: 0.7528 (mm) REVERT: B 59 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: B 61 MET cc_start: 0.8951 (pp-130) cc_final: 0.8653 (ppp) REVERT: B 134 ARG cc_start: 0.7383 (ptp-110) cc_final: 0.6974 (ptp-170) REVERT: B 262 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7188 (mpt) REVERT: B 270 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7717 (pp) REVERT: B 290 ASP cc_start: 0.7645 (m-30) cc_final: 0.7429 (m-30) REVERT: N 68 PHE cc_start: 0.6762 (m-10) cc_final: 0.6510 (m-80) REVERT: N 80 TYR cc_start: 0.7276 (m-10) cc_final: 0.7029 (m-80) REVERT: R 188 PHE cc_start: 0.7509 (m-10) cc_final: 0.6994 (t80) REVERT: R 302 ARG cc_start: 0.6885 (mtp180) cc_final: 0.6249 (mmt-90) REVERT: R 326 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.5645 (mp0) REVERT: R 338 LYS cc_start: 0.7907 (mttm) cc_final: 0.6928 (tttp) outliers start: 29 outliers final: 18 residues processed: 128 average time/residue: 1.8272 time to fit residues: 249.8676 Evaluate side-chains 136 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 75 GLN 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 37 LEU Chi-restraints excluded: chain N residue 4 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 362 LEU Chi-restraints excluded: chain R residue 412 PHE 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: 0.7980 chunk 69 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** 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 = 0.4201 r_free = 0.4201 target = 0.193871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154753 restraints weight = 9718.235| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.38 r_work: 0.3551 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8741 Z= 0.116 Angle : 0.511 6.414 11829 Z= 0.269 Chirality : 0.040 0.151 1317 Planarity : 0.004 0.055 1503 Dihedral : 3.992 18.461 1170 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.56 % Allowed : 18.90 % 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: 0.27 (0.26), residues: 1052 helix: 1.69 (0.26), residues: 420 sheet: 0.11 (0.36), residues: 195 loop : -1.32 (0.29), residues: 437 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 0.027 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 400) hydrogen bonds : angle 3.93539 ( 1152) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.81184 ( 4) covalent geometry : bond 0.00257 ( 8739) covalent geometry : angle 0.51121 (11825) *********************** 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 144 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.029 Fit side-chains REVERT: A 211 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7751 (pttm) REVERT: A 220 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: A 268 GLU cc_start: 0.7633 (mp0) cc_final: 0.7318 (mm-30) REVERT: A 341 ILE cc_start: 0.7718 (mm) cc_final: 0.7420 (mm) REVERT: B 59 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: B 61 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8665 (ppp) REVERT: B 88 ASN cc_start: 0.8208 (m110) cc_final: 0.7944 (p0) REVERT: B 134 ARG cc_start: 0.7284 (ptp-110) cc_final: 0.6857 (ptp-170) REVERT: B 262 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7109 (mpt) REVERT: B 270 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7684 (pp) REVERT: G 47 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5264 (mp0) REVERT: N 80 TYR cc_start: 0.7268 (m-10) cc_final: 0.6989 (m-80) REVERT: P 10 MET cc_start: 0.7450 (tpp) cc_final: 0.7190 (tpt) REVERT: R 188 PHE cc_start: 0.7404 (m-10) cc_final: 0.6876 (t80) REVERT: R 302 ARG cc_start: 0.6852 (mtp180) cc_final: 0.6116 (mmt-90) REVERT: R 326 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.5593 (mp0) REVERT: R 338 LYS cc_start: 0.7815 (mttm) cc_final: 0.6829 (tttp) REVERT: R 348 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5940 (ttt) outliers start: 33 outliers final: 17 residues processed: 127 average time/residue: 1.6220 time to fit residues: 221.4785 Evaluate side-chains 136 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 220 HIS 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 171 ILE 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 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 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: 0.8980 chunk 90 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.191923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152819 restraints weight = 9755.690| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.32 r_work: 0.3635 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8741 Z= 0.109 Angle : 0.509 6.435 11829 Z= 0.268 Chirality : 0.040 0.181 1317 Planarity : 0.004 0.055 1503 Dihedral : 3.957 18.393 1170 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.24 % Allowed : 19.44 % 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: 0.35 (0.26), residues: 1052 helix: 1.79 (0.26), residues: 416 sheet: 0.11 (0.36), residues: 195 loop : -1.25 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.009 0.001 HIS A 220 PHE 0.028 0.001 PHE R 202 TYR 0.020 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 400) hydrogen bonds : angle 3.92400 ( 1152) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.76065 ( 4) covalent geometry : bond 0.00239 ( 8739) covalent geometry : angle 0.50864 (11825) *********************** 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 142 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.542 Fit side-chains REVERT: A 211 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7773 (pttm) REVERT: A 220 HIS cc_start: 0.7985 (m-70) cc_final: 0.7680 (t-90) REVERT: A 268 GLU cc_start: 0.7612 (mp0) cc_final: 0.7265 (mm-30) REVERT: A 341 ILE cc_start: 0.7793 (mm) cc_final: 0.7489 (mm) REVERT: B 59 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: B 61 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8641 (ppp) REVERT: B 134 ARG cc_start: 0.7351 (ptp-110) cc_final: 0.6952 (ptp-170) REVERT: B 262 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7181 (mpt) REVERT: B 270 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7710 (pp) REVERT: G 47 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5276 (mp0) REVERT: N 83 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6371 (mtp) REVERT: R 188 PHE cc_start: 0.7499 (m-10) cc_final: 0.6984 (t80) REVERT: R 302 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6212 (mmt-90) REVERT: R 326 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5681 (mp0) REVERT: R 338 LYS cc_start: 0.7886 (mttm) cc_final: 0.6935 (tttp) outliers start: 30 outliers final: 17 residues processed: 126 average time/residue: 2.1797 time to fit residues: 295.0874 Evaluate side-chains 133 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 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 75 GLN 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 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET 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 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: 0.3980 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 220 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153597 restraints weight = 9563.290| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.19 r_work: 0.3672 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8741 Z= 0.105 Angle : 0.504 6.573 11829 Z= 0.266 Chirality : 0.040 0.170 1317 Planarity : 0.004 0.054 1503 Dihedral : 3.937 17.998 1170 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.13 % Allowed : 19.44 % 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: 0.43 (0.26), residues: 1052 helix: 1.86 (0.26), residues: 415 sheet: 0.27 (0.37), residues: 190 loop : -1.25 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.003 0.001 HIS R 428 PHE 0.030 0.001 PHE R 202 TYR 0.019 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 400) hydrogen bonds : angle 3.87920 ( 1152) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.70041 ( 4) covalent geometry : bond 0.00224 ( 8739) covalent geometry : angle 0.50409 (11825) ********************** 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 140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.712 Fit side-chains REVERT: A 211 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7807 (pttm) REVERT: A 268 GLU cc_start: 0.7596 (mp0) cc_final: 0.7290 (mm-30) REVERT: A 341 ILE cc_start: 0.7806 (mm) cc_final: 0.7495 (mm) REVERT: B 59 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: B 61 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8523 (pp-130) REVERT: B 134 ARG cc_start: 0.7393 (ptp-110) cc_final: 0.7009 (ptp-170) REVERT: B 262 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7212 (mpt) REVERT: B 270 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7730 (pp) REVERT: G 47 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5289 (mp0) REVERT: N 80 TYR cc_start: 0.7352 (m-80) cc_final: 0.6971 (m-80) REVERT: N 83 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.6173 (mtp) REVERT: R 188 PHE cc_start: 0.7524 (m-10) cc_final: 0.7038 (t80) REVERT: R 302 ARG cc_start: 0.6940 (mtp180) cc_final: 0.6260 (mmt-90) REVERT: R 326 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.5680 (mp0) REVERT: R 338 LYS cc_start: 0.7891 (mttm) cc_final: 0.6999 (tttp) outliers start: 29 outliers final: 16 residues processed: 125 average time/residue: 1.3919 time to fit residues: 185.9741 Evaluate side-chains 132 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 75 GLN 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 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET 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 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: 0.8980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.0020 chunk 15 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 220 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.194575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154728 restraints weight = 9552.058| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.19 r_work: 0.3678 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8741 Z= 0.102 Angle : 0.501 6.519 11829 Z= 0.265 Chirality : 0.040 0.193 1317 Planarity : 0.004 0.054 1503 Dihedral : 3.928 22.262 1170 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.24 % Allowed : 19.44 % 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: 0.48 (0.27), residues: 1052 helix: 1.89 (0.27), residues: 416 sheet: 0.35 (0.37), residues: 190 loop : -1.26 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS R 428 PHE 0.031 0.001 PHE R 202 TYR 0.019 0.001 TYR R 182 ARG 0.002 0.000 ARG R 344 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 400) hydrogen bonds : angle 3.85479 ( 1152) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.67069 ( 4) covalent geometry : bond 0.00215 ( 8739) covalent geometry : angle 0.50125 (11825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8379.98 seconds wall clock time: 154 minutes 29.04 seconds (9269.04 seconds total)