Starting phenix.real_space_refine on Sat Aug 23 00:25:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7evm_31329/08_2025/7evm_31329_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evm_31329/08_2025/7evm_31329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7evm_31329/08_2025/7evm_31329_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evm_31329/08_2025/7evm_31329_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7evm_31329/08_2025/7evm_31329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evm_31329/08_2025/7evm_31329.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 2 4.86 5 C 5445 2.51 5 N 1445 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8462 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1957 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2330 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 5, 'TRANS': 276} Chain breaks: 2 Chain: "R" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 185 Unusual residues: {'CLR': 6, 'HNO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 1.96, per 1000 atoms: 0.23 Number of scatterers: 8462 At special positions: 0 Unit cell: (82.555, 95.095, 131.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 48 16.00 O 1522 8.00 N 1445 7.00 C 5445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.06 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 508.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.736A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.723A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.912A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.638A pdb=" N TRP A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.628A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.567A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.938A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.567A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.753A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 143 Processing helix chain 'R' and resid 144 through 169 removed outlier: 3.773A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 211 removed outlier: 4.169A pdb=" N GLN R 211 " --> pdb=" O THR R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 222 removed outlier: 3.911A pdb=" N GLN R 221 " --> pdb=" O LEU R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 257 Processing helix chain 'R' and resid 263 through 292 removed outlier: 3.623A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.544A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.501A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 removed outlier: 3.714A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 368 removed outlier: 4.023A pdb=" N PHE R 367 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 404 removed outlier: 3.553A pdb=" N THR R 386 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 424 removed outlier: 3.867A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS R 424 " --> pdb=" O TRP R 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.105A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.722A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.133A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.748A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.601A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.646A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.841A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.762A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.090A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1938 1.33 - 1.45: 2088 1.45 - 1.58: 4557 1.58 - 1.71: 5 1.71 - 1.83: 68 Bond restraints: 8656 Sorted by residual: bond pdb=" C14 HNO R 501 " pdb=" N15 HNO R 501 " ideal model delta sigma weight residual 1.348 1.458 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 1.527 1.474 0.053 1.32e-02 5.74e+03 1.59e+01 bond pdb=" C13 CLR R 506 " pdb=" C18 CLR R 506 " ideal model delta sigma weight residual 1.532 1.597 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C LEU R 311 " pdb=" O LEU R 311 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.07e+01 bond pdb=" C13 CLR R 507 " pdb=" C18 CLR R 507 " ideal model delta sigma weight residual 1.532 1.597 -0.065 2.00e-02 2.50e+03 1.04e+01 ... (remaining 8651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11531 2.63 - 5.26: 190 5.26 - 7.89: 31 7.89 - 10.52: 5 10.52 - 13.15: 1 Bond angle restraints: 11758 Sorted by residual: angle pdb=" N PHE R 143 " pdb=" CA PHE R 143 " pdb=" C PHE R 143 " ideal model delta sigma weight residual 112.92 99.77 13.15 1.23e+00 6.61e-01 1.14e+02 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 110.42 103.67 6.75 9.60e-01 1.09e+00 4.94e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 114.03 122.66 -8.63 1.23e+00 6.61e-01 4.93e+01 angle pdb=" N GLU R 292 " pdb=" CA GLU R 292 " pdb=" C GLU R 292 " ideal model delta sigma weight residual 110.17 120.09 -9.92 1.51e+00 4.39e-01 4.31e+01 angle pdb=" N LEU R 411 " pdb=" CA LEU R 411 " pdb=" C LEU R 411 " ideal model delta sigma weight residual 111.24 104.26 6.98 1.29e+00 6.01e-01 2.93e+01 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 4745 17.00 - 34.01: 495 34.01 - 51.01: 123 51.01 - 68.01: 34 68.01 - 85.02: 8 Dihedral angle restraints: 5405 sinusoidal: 2383 harmonic: 3022 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 160.72 -67.72 1 1.00e+01 1.00e-02 5.96e+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 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -132.03 9.43 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1158 0.079 - 0.159: 142 0.159 - 0.238: 14 0.238 - 0.318: 5 0.318 - 0.397: 6 Chirality restraints: 1325 Sorted by residual: chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA GLU R 292 " pdb=" N GLU R 292 " pdb=" C GLU R 292 " pdb=" CB GLU R 292 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C14 CLR R 505 " pdb=" C13 CLR R 505 " pdb=" C15 CLR R 505 " pdb=" C8 CLR R 505 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 1322 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 410 " 0.025 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C GLN R 410 " -0.090 2.00e-02 2.50e+03 pdb=" O GLN R 410 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU R 411 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 198 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ASP R 198 " -0.078 2.00e-02 2.50e+03 pdb=" O ASP R 198 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA R 199 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 98 " 0.020 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG N 98 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG N 98 " 0.030 2.00e-02 2.50e+03 pdb=" N CYS N 99 " 0.025 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 438 2.72 - 3.26: 8758 3.26 - 3.81: 14360 3.81 - 4.35: 18359 4.35 - 4.90: 30257 Nonbonded interactions: 72172 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.175 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.222 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.265 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.282 3.040 ... (remaining 72167 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: 0.980 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 8660 Z= 0.306 Angle : 0.861 13.151 11764 Z= 0.502 Chirality : 0.061 0.397 1325 Planarity : 0.005 0.052 1454 Dihedral : 15.260 85.018 3442 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.36 % Allowed : 7.51 % Favored : 89.13 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.24), residues: 1019 helix: -1.35 (0.23), residues: 384 sheet: -1.43 (0.31), residues: 209 loop : -1.41 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 129 TYR 0.028 0.002 TYR R 148 PHE 0.017 0.002 PHE R 280 TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8656) covalent geometry : angle 0.85485 (11758) SS BOND : bond 0.02199 ( 3) SS BOND : angle 4.61878 ( 6) hydrogen bonds : bond 0.20724 ( 419) hydrogen bonds : angle 7.81685 ( 1188) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8536 (tt0) cc_final: 0.8030 (tt0) REVERT: A 215 ASP cc_start: 0.7802 (t0) cc_final: 0.7307 (t0) REVERT: A 325 THR cc_start: 0.8755 (m) cc_final: 0.8499 (p) REVERT: A 339 TYR cc_start: 0.7798 (m-80) cc_final: 0.7526 (m-80) REVERT: A 343 ASP cc_start: 0.8072 (m-30) cc_final: 0.7510 (m-30) REVERT: A 370 GLU cc_start: 0.7996 (pm20) cc_final: 0.7757 (pp20) REVERT: A 378 ASP cc_start: 0.7259 (m-30) cc_final: 0.6767 (m-30) REVERT: A 381 ASP cc_start: 0.8350 (t0) cc_final: 0.8112 (t0) REVERT: B 44 GLN cc_start: 0.7955 (pt0) cc_final: 0.7693 (pt0) REVERT: B 47 THR cc_start: 0.8847 (t) cc_final: 0.8562 (m) REVERT: B 124 TYR cc_start: 0.8361 (m-80) cc_final: 0.7914 (m-80) REVERT: B 132 ASN cc_start: 0.6821 (p0) cc_final: 0.6370 (p0) REVERT: B 138 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 175 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7223 (pp30) REVERT: B 217 MET cc_start: 0.7127 (ptt) cc_final: 0.6894 (ptt) REVERT: B 226 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 228 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: B 230 ASN cc_start: 0.8282 (m-40) cc_final: 0.8033 (m-40) REVERT: B 243 THR cc_start: 0.7847 (p) cc_final: 0.7568 (p) REVERT: B 291 ASP cc_start: 0.7545 (p0) cc_final: 0.7336 (p0) REVERT: B 312 ASP cc_start: 0.8278 (m-30) cc_final: 0.7994 (m-30) REVERT: G 21 MET cc_start: 0.7174 (tpt) cc_final: 0.6694 (ttp) REVERT: N 3 GLN cc_start: 0.7288 (tp40) cc_final: 0.6468 (tm-30) REVERT: N 31 ASN cc_start: 0.7938 (m-40) cc_final: 0.7695 (t0) REVERT: N 77 ASN cc_start: 0.7551 (m-40) cc_final: 0.7238 (p0) REVERT: R 136 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7166 (p) REVERT: R 142 LEU cc_start: 0.8305 (tp) cc_final: 0.8034 (tm) REVERT: R 144 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7534 (tp) REVERT: R 148 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5614 (p90) REVERT: R 197 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7718 (tmmm) REVERT: R 262 GLU cc_start: 0.8326 (pt0) cc_final: 0.7912 (pt0) REVERT: R 346 LYS cc_start: 0.7558 (mttt) cc_final: 0.6956 (pttm) REVERT: R 383 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8330 (tmtp) REVERT: R 412 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: R 423 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6888 (pt0) outliers start: 30 outliers final: 4 residues processed: 301 average time/residue: 0.5381 time to fit residues: 171.7422 Evaluate side-chains 162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 421 ARG Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 156 GLN B 220 GLN B 259 GLN N 35 ASN R 171 HIS R 263 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099356 restraints weight = 12554.899| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.85 r_work: 0.3195 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8660 Z= 0.152 Angle : 0.621 7.725 11764 Z= 0.327 Chirality : 0.044 0.162 1325 Planarity : 0.005 0.087 1454 Dihedral : 8.458 63.916 1557 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.04 % Allowed : 19.39 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.26), residues: 1019 helix: -0.02 (0.25), residues: 399 sheet: -0.87 (0.33), residues: 209 loop : -1.03 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.027 0.002 TYR R 148 PHE 0.022 0.002 PHE A 273 TRP 0.013 0.002 TRP B 339 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8656) covalent geometry : angle 0.61935 (11758) SS BOND : bond 0.00307 ( 3) SS BOND : angle 2.06836 ( 6) hydrogen bonds : bond 0.04367 ( 419) hydrogen bonds : angle 5.27320 ( 1188) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8014 (tp40) cc_final: 0.7792 (tp-100) REVERT: A 60 MET cc_start: 0.8043 (mtt) cc_final: 0.7699 (mpt) REVERT: A 213 GLN cc_start: 0.8804 (tt0) cc_final: 0.8234 (tt0) REVERT: A 215 ASP cc_start: 0.7797 (t0) cc_final: 0.7285 (t0) REVERT: A 278 ASN cc_start: 0.7443 (m-40) cc_final: 0.7124 (m-40) REVERT: A 294 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7569 (mm110) REVERT: A 325 THR cc_start: 0.8848 (m) cc_final: 0.8538 (p) REVERT: A 343 ASP cc_start: 0.8306 (m-30) cc_final: 0.7786 (m-30) REVERT: A 352 SER cc_start: 0.8086 (t) cc_final: 0.6841 (t) REVERT: A 370 GLU cc_start: 0.7989 (pm20) cc_final: 0.7665 (pm20) REVERT: A 378 ASP cc_start: 0.7460 (m-30) cc_final: 0.7237 (m-30) REVERT: B 13 GLN cc_start: 0.8131 (mm110) cc_final: 0.7914 (mm110) REVERT: B 38 ASP cc_start: 0.8559 (p0) cc_final: 0.8013 (p0) REVERT: B 44 GLN cc_start: 0.8213 (pt0) cc_final: 0.7915 (pt0) REVERT: B 57 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8200 (ptpp) REVERT: B 124 TYR cc_start: 0.8645 (m-80) cc_final: 0.8179 (m-80) REVERT: B 138 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 217 MET cc_start: 0.8032 (ptt) cc_final: 0.7659 (ptt) REVERT: B 228 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: B 230 ASN cc_start: 0.8531 (m-40) cc_final: 0.8319 (m110) REVERT: B 243 THR cc_start: 0.7859 (p) cc_final: 0.7453 (p) REVERT: G 38 MET cc_start: 0.7459 (ptp) cc_final: 0.7154 (ttp) REVERT: G 42 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7053 (mp0) REVERT: N 3 GLN cc_start: 0.7643 (tp40) cc_final: 0.6956 (tm-30) REVERT: N 31 ASN cc_start: 0.8267 (m-40) cc_final: 0.7896 (t0) REVERT: N 35 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8801 (p0) REVERT: N 77 ASN cc_start: 0.7605 (m-40) cc_final: 0.7334 (p0) REVERT: N 110 VAL cc_start: 0.8939 (m) cc_final: 0.8641 (t) REVERT: N 120 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8770 (tp40) REVERT: R 139 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8358 (tt0) REVERT: R 142 LEU cc_start: 0.8263 (tp) cc_final: 0.7971 (tm) REVERT: R 262 GLU cc_start: 0.8308 (pt0) cc_final: 0.7901 (pt0) REVERT: R 305 TYR cc_start: 0.7296 (m-80) cc_final: 0.7048 (m-10) REVERT: R 346 LYS cc_start: 0.7356 (mttt) cc_final: 0.6780 (pttm) REVERT: R 387 GLU cc_start: 0.8435 (tt0) cc_final: 0.7505 (mt-10) REVERT: R 394 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: R 407 ASN cc_start: 0.8897 (m-40) cc_final: 0.8549 (m110) outliers start: 36 outliers final: 11 residues processed: 199 average time/residue: 0.5542 time to fit residues: 117.2733 Evaluate side-chains 161 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 371 ASN B 176 GLN R 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.135743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102834 restraints weight = 13350.431| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.77 r_work: 0.3240 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8660 Z= 0.141 Angle : 0.580 7.571 11764 Z= 0.307 Chirality : 0.043 0.145 1325 Planarity : 0.005 0.062 1454 Dihedral : 7.203 59.129 1533 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.04 % Allowed : 21.41 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.26), residues: 1019 helix: 0.58 (0.26), residues: 399 sheet: -0.67 (0.34), residues: 209 loop : -0.94 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 421 TYR 0.022 0.002 TYR R 148 PHE 0.030 0.002 PHE N 27 TRP 0.027 0.002 TRP A 277 HIS 0.004 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8656) covalent geometry : angle 0.57920 (11758) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.63388 ( 6) hydrogen bonds : bond 0.03835 ( 419) hydrogen bonds : angle 4.85537 ( 1188) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6304 (pt0) REVERT: A 213 GLN cc_start: 0.8809 (tt0) cc_final: 0.8249 (tt0) REVERT: A 215 ASP cc_start: 0.7778 (t0) cc_final: 0.7216 (t0) REVERT: A 220 HIS cc_start: 0.7486 (m90) cc_final: 0.7136 (m90) REVERT: A 278 ASN cc_start: 0.7815 (m-40) cc_final: 0.7427 (m-40) REVERT: A 296 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 325 THR cc_start: 0.8898 (m) cc_final: 0.8624 (p) REVERT: A 343 ASP cc_start: 0.8413 (m-30) cc_final: 0.8006 (m-30) REVERT: A 370 GLU cc_start: 0.7999 (pm20) cc_final: 0.7682 (pm20) REVERT: B 13 GLN cc_start: 0.8179 (mm110) cc_final: 0.7921 (mm110) REVERT: B 19 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.8176 (ttp80) REVERT: B 38 ASP cc_start: 0.8530 (p0) cc_final: 0.7968 (p0) REVERT: B 44 GLN cc_start: 0.8264 (pt0) cc_final: 0.7977 (pt0) REVERT: B 57 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8423 (ptpp) REVERT: B 138 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8257 (mt-10) REVERT: B 172 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 226 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 228 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: B 230 ASN cc_start: 0.8573 (m-40) cc_final: 0.8357 (m110) REVERT: B 243 THR cc_start: 0.8051 (p) cc_final: 0.7645 (p) REVERT: G 21 MET cc_start: 0.7255 (ttp) cc_final: 0.6739 (ttp) REVERT: G 38 MET cc_start: 0.7603 (ptp) cc_final: 0.7307 (ttp) REVERT: G 42 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7415 (mp0) REVERT: N 3 GLN cc_start: 0.7637 (tp40) cc_final: 0.6967 (tm-30) REVERT: N 5 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7486 (tp-100) REVERT: N 31 ASN cc_start: 0.8352 (m-40) cc_final: 0.8070 (t0) REVERT: N 35 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8841 (p0) REVERT: N 77 ASN cc_start: 0.7650 (m-40) cc_final: 0.7200 (p0) REVERT: N 105 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7741 (ttp-110) REVERT: N 110 VAL cc_start: 0.8962 (m) cc_final: 0.8702 (t) REVERT: N 120 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8735 (tp40) REVERT: R 139 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8376 (tt0) REVERT: R 142 LEU cc_start: 0.8256 (tp) cc_final: 0.8002 (tm) REVERT: R 262 GLU cc_start: 0.8283 (pt0) cc_final: 0.8024 (pt0) REVERT: R 346 LYS cc_start: 0.7536 (mttt) cc_final: 0.6944 (pttm) REVERT: R 394 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: R 412 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: R 423 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5908 (tm-30) outliers start: 36 outliers final: 11 residues processed: 189 average time/residue: 0.5484 time to fit residues: 110.3471 Evaluate side-chains 168 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 83 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN N 1 GLN N 35 ASN R 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101126 restraints weight = 13626.034| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.82 r_work: 0.3241 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8660 Z= 0.148 Angle : 0.556 7.649 11764 Z= 0.293 Chirality : 0.043 0.156 1325 Planarity : 0.004 0.045 1454 Dihedral : 7.032 59.873 1533 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.60 % Allowed : 21.86 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.26), residues: 1019 helix: 0.91 (0.26), residues: 405 sheet: -0.57 (0.34), residues: 216 loop : -0.84 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.020 0.002 TYR R 148 PHE 0.021 0.001 PHE N 27 TRP 0.019 0.001 TRP A 277 HIS 0.004 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8656) covalent geometry : angle 0.55466 (11758) SS BOND : bond 0.00606 ( 3) SS BOND : angle 1.50606 ( 6) hydrogen bonds : bond 0.03669 ( 419) hydrogen bonds : angle 4.69001 ( 1188) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8745 (tt0) cc_final: 0.8180 (tt0) REVERT: A 215 ASP cc_start: 0.7760 (t0) cc_final: 0.7216 (t0) REVERT: A 325 THR cc_start: 0.8927 (m) cc_final: 0.8661 (p) REVERT: A 343 ASP cc_start: 0.8401 (m-30) cc_final: 0.8062 (m-30) REVERT: A 370 GLU cc_start: 0.7951 (pm20) cc_final: 0.7600 (pm20) REVERT: B 13 GLN cc_start: 0.8244 (mm110) cc_final: 0.7960 (mm110) REVERT: B 19 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8173 (ttp80) REVERT: B 38 ASP cc_start: 0.8538 (p0) cc_final: 0.7998 (p0) REVERT: B 44 GLN cc_start: 0.8305 (pt0) cc_final: 0.7983 (pt0) REVERT: B 57 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8452 (ptpp) REVERT: B 138 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8307 (mt-10) REVERT: B 172 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 214 ARG cc_start: 0.8372 (mtm110) cc_final: 0.8140 (mtm110) REVERT: B 215 GLU cc_start: 0.8047 (mp0) cc_final: 0.7517 (mp0) REVERT: B 228 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: B 230 ASN cc_start: 0.8607 (m-40) cc_final: 0.8380 (m110) REVERT: B 243 THR cc_start: 0.8091 (p) cc_final: 0.7669 (p) REVERT: G 21 MET cc_start: 0.7381 (ttp) cc_final: 0.7137 (ttp) REVERT: G 38 MET cc_start: 0.7749 (ptp) cc_final: 0.7412 (ttp) REVERT: G 42 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7526 (mp0) REVERT: N 3 GLN cc_start: 0.7681 (tp40) cc_final: 0.7004 (tm-30) REVERT: N 31 ASN cc_start: 0.8416 (m-40) cc_final: 0.8098 (t0) REVERT: N 67 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.5187 (ptm-80) REVERT: N 77 ASN cc_start: 0.7677 (m-40) cc_final: 0.7126 (p0) REVERT: N 90 ASP cc_start: 0.8755 (m-30) cc_final: 0.8540 (m-30) REVERT: N 110 VAL cc_start: 0.8965 (m) cc_final: 0.8748 (t) REVERT: N 120 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8777 (tp40) REVERT: R 139 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8394 (tt0) REVERT: R 142 LEU cc_start: 0.8215 (tp) cc_final: 0.7971 (tm) REVERT: R 148 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6531 (p90) REVERT: R 203 TRP cc_start: 0.7147 (t-100) cc_final: 0.6924 (t-100) REVERT: R 260 LEU cc_start: 0.8162 (pt) cc_final: 0.7798 (mm) REVERT: R 346 LYS cc_start: 0.7515 (mttt) cc_final: 0.6923 (pttm) REVERT: R 394 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: R 412 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7518 (tm-30) REVERT: R 413 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: R 423 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5918 (tm-30) outliers start: 41 outliers final: 15 residues processed: 180 average time/residue: 0.6174 time to fit residues: 118.2328 Evaluate side-chains 166 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain R residue 423 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099365 restraints weight = 13389.389| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.82 r_work: 0.3209 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8660 Z= 0.148 Angle : 0.553 7.339 11764 Z= 0.289 Chirality : 0.042 0.165 1325 Planarity : 0.004 0.043 1454 Dihedral : 6.856 59.884 1533 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.04 % Allowed : 23.32 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.27), residues: 1019 helix: 1.12 (0.26), residues: 405 sheet: -0.52 (0.34), residues: 216 loop : -0.79 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.017 0.001 TYR N 95 PHE 0.034 0.002 PHE N 27 TRP 0.021 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8656) covalent geometry : angle 0.55213 (11758) SS BOND : bond 0.00337 ( 3) SS BOND : angle 1.38618 ( 6) hydrogen bonds : bond 0.03552 ( 419) hydrogen bonds : angle 4.56319 ( 1188) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8065 (mmtm) REVERT: A 213 GLN cc_start: 0.8788 (tt0) cc_final: 0.8192 (tt0) REVERT: A 215 ASP cc_start: 0.7707 (t0) cc_final: 0.7172 (t0) REVERT: A 325 THR cc_start: 0.8962 (m) cc_final: 0.8757 (p) REVERT: A 343 ASP cc_start: 0.8431 (m-30) cc_final: 0.8109 (m-30) REVERT: A 370 GLU cc_start: 0.7949 (pm20) cc_final: 0.7609 (pm20) REVERT: B 13 GLN cc_start: 0.8256 (mm110) cc_final: 0.7983 (mm110) REVERT: B 19 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.8156 (ttp80) REVERT: B 38 ASP cc_start: 0.8535 (p0) cc_final: 0.7977 (p0) REVERT: B 57 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8487 (ptpp) REVERT: B 138 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 172 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: B 215 GLU cc_start: 0.8113 (mp0) cc_final: 0.7582 (mp0) REVERT: B 243 THR cc_start: 0.8087 (p) cc_final: 0.7667 (p) REVERT: G 20 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7202 (ttpp) REVERT: G 21 MET cc_start: 0.7532 (ttp) cc_final: 0.6801 (ttp) REVERT: G 38 MET cc_start: 0.7799 (ptp) cc_final: 0.6161 (ttp) REVERT: G 42 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7236 (mp0) REVERT: N 3 GLN cc_start: 0.7657 (tp40) cc_final: 0.6990 (tm-30) REVERT: N 31 ASN cc_start: 0.8468 (m-40) cc_final: 0.8198 (t0) REVERT: N 67 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.5311 (ptm-80) REVERT: N 90 ASP cc_start: 0.8719 (m-30) cc_final: 0.8514 (m-30) REVERT: N 120 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8764 (tp40) REVERT: R 139 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8340 (tt0) REVERT: R 142 LEU cc_start: 0.8217 (tp) cc_final: 0.7981 (tm) REVERT: R 148 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6773 (p90) REVERT: R 260 LEU cc_start: 0.8182 (pt) cc_final: 0.7844 (mm) REVERT: R 346 LYS cc_start: 0.7532 (mttt) cc_final: 0.6940 (pttm) REVERT: R 394 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: R 410 GLN cc_start: 0.8525 (mt0) cc_final: 0.8105 (mt0) REVERT: R 414 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.6134 (mpt180) outliers start: 36 outliers final: 21 residues processed: 187 average time/residue: 0.5965 time to fit residues: 118.7896 Evaluate side-chains 184 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN ** N 35 ASN ** 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 = 0.3785 r_free = 0.3785 target = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097298 restraints weight = 13322.803| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.84 r_work: 0.3200 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8660 Z= 0.162 Angle : 0.576 7.690 11764 Z= 0.299 Chirality : 0.042 0.160 1325 Planarity : 0.004 0.045 1454 Dihedral : 6.654 59.844 1528 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.26 % Allowed : 24.33 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.27), residues: 1019 helix: 1.24 (0.26), residues: 406 sheet: -0.44 (0.34), residues: 222 loop : -0.73 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 105 TYR 0.019 0.002 TYR N 32 PHE 0.055 0.002 PHE N 27 TRP 0.023 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8656) covalent geometry : angle 0.57480 (11758) SS BOND : bond 0.00163 ( 3) SS BOND : angle 1.54382 ( 6) hydrogen bonds : bond 0.03512 ( 419) hydrogen bonds : angle 4.55357 ( 1188) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7947 (mmtm) REVERT: A 213 GLN cc_start: 0.8792 (tt0) cc_final: 0.8242 (tt0) REVERT: A 215 ASP cc_start: 0.7721 (t0) cc_final: 0.7198 (t0) REVERT: A 325 THR cc_start: 0.8933 (m) cc_final: 0.8724 (p) REVERT: A 343 ASP cc_start: 0.8443 (m-30) cc_final: 0.8109 (m-30) REVERT: A 370 GLU cc_start: 0.7962 (pm20) cc_final: 0.7635 (pm20) REVERT: B 13 GLN cc_start: 0.8244 (mm110) cc_final: 0.7936 (mm110) REVERT: B 19 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.8174 (ttp80) REVERT: B 38 ASP cc_start: 0.8584 (p0) cc_final: 0.8054 (p0) REVERT: B 57 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8490 (ptpp) REVERT: B 138 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8470 (mt-10) REVERT: B 169 TRP cc_start: 0.9127 (m100) cc_final: 0.8866 (m100) REVERT: B 172 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: B 215 GLU cc_start: 0.8073 (mp0) cc_final: 0.7739 (mp0) REVERT: B 228 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: B 243 THR cc_start: 0.8076 (p) cc_final: 0.7624 (p) REVERT: G 21 MET cc_start: 0.7596 (ttp) cc_final: 0.6865 (ttp) REVERT: G 38 MET cc_start: 0.7881 (ptp) cc_final: 0.6115 (ttp) REVERT: G 42 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7329 (mp0) REVERT: N 3 GLN cc_start: 0.7643 (tp40) cc_final: 0.6993 (tm-30) REVERT: N 31 ASN cc_start: 0.8470 (m-40) cc_final: 0.8149 (t0) REVERT: N 67 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.5082 (ptm-80) REVERT: N 90 ASP cc_start: 0.8772 (m-30) cc_final: 0.8552 (m-30) REVERT: N 117 TYR cc_start: 0.8062 (m-80) cc_final: 0.7818 (m-80) REVERT: N 120 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8695 (tp40) REVERT: R 139 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8404 (tt0) REVERT: R 142 LEU cc_start: 0.8306 (tp) cc_final: 0.8022 (tm) REVERT: R 146 ILE cc_start: 0.6668 (tt) cc_final: 0.6363 (tp) REVERT: R 148 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6793 (p90) REVERT: R 262 GLU cc_start: 0.8229 (pt0) cc_final: 0.7607 (pm20) REVERT: R 346 LYS cc_start: 0.7580 (mttt) cc_final: 0.6988 (pttm) REVERT: R 388 LEU cc_start: 0.8239 (mm) cc_final: 0.7890 (mt) REVERT: R 394 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: R 414 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5966 (mpt180) REVERT: R 423 GLU cc_start: 0.6310 (tm-30) cc_final: 0.6104 (tm-30) outliers start: 38 outliers final: 21 residues processed: 184 average time/residue: 0.5855 time to fit residues: 114.8175 Evaluate side-chains 182 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097706 restraints weight = 13386.722| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.85 r_work: 0.3208 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8660 Z= 0.148 Angle : 0.564 7.316 11764 Z= 0.294 Chirality : 0.042 0.149 1325 Planarity : 0.004 0.043 1454 Dihedral : 6.611 59.622 1528 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.48 % Allowed : 25.00 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.27), residues: 1019 helix: 1.32 (0.26), residues: 406 sheet: -0.46 (0.35), residues: 218 loop : -0.68 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.021 0.002 TYR N 32 PHE 0.061 0.002 PHE N 27 TRP 0.022 0.002 TRP A 277 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8656) covalent geometry : angle 0.56271 (11758) SS BOND : bond 0.00092 ( 3) SS BOND : angle 1.61523 ( 6) hydrogen bonds : bond 0.03446 ( 419) hydrogen bonds : angle 4.51699 ( 1188) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8388 (pp20) cc_final: 0.8109 (pp20) REVERT: A 211 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7966 (mmtm) REVERT: A 215 ASP cc_start: 0.7692 (t0) cc_final: 0.7179 (t0) REVERT: A 325 THR cc_start: 0.8941 (m) cc_final: 0.8734 (p) REVERT: A 343 ASP cc_start: 0.8451 (m-30) cc_final: 0.8112 (m-30) REVERT: A 370 GLU cc_start: 0.7943 (pm20) cc_final: 0.7623 (pm20) REVERT: B 13 GLN cc_start: 0.8256 (mm110) cc_final: 0.7948 (mm110) REVERT: B 19 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8162 (ttp80) REVERT: B 38 ASP cc_start: 0.8593 (p0) cc_final: 0.8102 (p0) REVERT: B 57 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8499 (ptpp) REVERT: B 138 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8481 (mt-10) REVERT: B 169 TRP cc_start: 0.9111 (m100) cc_final: 0.8824 (m100) REVERT: B 172 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 198 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 215 GLU cc_start: 0.8178 (mp0) cc_final: 0.7469 (mp0) REVERT: B 228 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 243 THR cc_start: 0.8121 (p) cc_final: 0.7707 (p) REVERT: G 20 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7318 (tmmt) REVERT: G 21 MET cc_start: 0.7684 (ttp) cc_final: 0.7068 (ttp) REVERT: G 38 MET cc_start: 0.7934 (ptp) cc_final: 0.6338 (ptp) REVERT: G 42 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7325 (mp0) REVERT: N 3 GLN cc_start: 0.7632 (tp40) cc_final: 0.6975 (tm-30) REVERT: N 31 ASN cc_start: 0.8422 (m-40) cc_final: 0.8063 (t0) REVERT: N 32 TYR cc_start: 0.5622 (p90) cc_final: 0.5416 (p90) REVERT: N 34 MET cc_start: 0.8959 (mmm) cc_final: 0.8491 (mmm) REVERT: N 67 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.5032 (ptm-80) REVERT: N 90 ASP cc_start: 0.8747 (m-30) cc_final: 0.8529 (m-30) REVERT: N 117 TYR cc_start: 0.8005 (m-80) cc_final: 0.7748 (m-80) REVERT: R 139 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8361 (tt0) REVERT: R 142 LEU cc_start: 0.8288 (tp) cc_final: 0.8042 (tm) REVERT: R 146 ILE cc_start: 0.6853 (tt) cc_final: 0.6576 (tp) REVERT: R 148 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6869 (p90) REVERT: R 260 LEU cc_start: 0.8219 (pt) cc_final: 0.7918 (mm) REVERT: R 262 GLU cc_start: 0.8188 (pt0) cc_final: 0.7576 (pm20) REVERT: R 299 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7537 (ttm170) REVERT: R 346 LYS cc_start: 0.7599 (mttt) cc_final: 0.7002 (pttm) REVERT: R 394 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: R 406 ASN cc_start: 0.7722 (t0) cc_final: 0.6668 (t0) REVERT: R 408 GLU cc_start: 0.7935 (mp0) cc_final: 0.7491 (mp0) REVERT: R 412 GLU cc_start: 0.7996 (tp30) cc_final: 0.7771 (tm-30) REVERT: R 414 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5969 (mpt180) outliers start: 40 outliers final: 20 residues processed: 187 average time/residue: 0.5734 time to fit residues: 114.4106 Evaluate side-chains 185 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 0.0040 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098799 restraints weight = 13236.121| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.83 r_work: 0.3205 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8660 Z= 0.140 Angle : 0.564 7.314 11764 Z= 0.295 Chirality : 0.042 0.144 1325 Planarity : 0.004 0.053 1454 Dihedral : 6.541 59.555 1528 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.26 % Allowed : 25.56 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.27), residues: 1019 helix: 1.40 (0.27), residues: 404 sheet: -0.34 (0.36), residues: 212 loop : -0.59 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.019 0.002 TYR N 32 PHE 0.046 0.001 PHE N 27 TRP 0.021 0.001 TRP A 277 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8656) covalent geometry : angle 0.56326 (11758) SS BOND : bond 0.00147 ( 3) SS BOND : angle 1.37799 ( 6) hydrogen bonds : bond 0.03433 ( 419) hydrogen bonds : angle 4.54101 ( 1188) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7682 (t0) cc_final: 0.7165 (t0) REVERT: A 343 ASP cc_start: 0.8449 (m-30) cc_final: 0.8073 (m-30) REVERT: A 370 GLU cc_start: 0.7907 (pm20) cc_final: 0.7603 (pm20) REVERT: B 13 GLN cc_start: 0.8244 (mm110) cc_final: 0.7938 (mm110) REVERT: B 19 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8148 (ttp80) REVERT: B 38 ASP cc_start: 0.8600 (p0) cc_final: 0.8107 (p0) REVERT: B 57 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8413 (ptpp) REVERT: B 138 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 169 TRP cc_start: 0.9102 (m100) cc_final: 0.8829 (m100) REVERT: B 172 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 198 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8821 (mt) REVERT: B 215 GLU cc_start: 0.8138 (mp0) cc_final: 0.7776 (mp0) REVERT: B 226 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7159 (tt0) REVERT: B 228 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: B 243 THR cc_start: 0.8219 (p) cc_final: 0.7830 (p) REVERT: G 20 LYS cc_start: 0.7477 (ttpp) cc_final: 0.7270 (tmmt) REVERT: G 21 MET cc_start: 0.7662 (ttp) cc_final: 0.7045 (ttp) REVERT: G 38 MET cc_start: 0.7911 (ptp) cc_final: 0.7532 (ptp) REVERT: G 42 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7630 (mp0) REVERT: N 3 GLN cc_start: 0.7611 (tp40) cc_final: 0.6940 (tm-30) REVERT: N 31 ASN cc_start: 0.8409 (m-40) cc_final: 0.8047 (t0) REVERT: N 32 TYR cc_start: 0.6032 (p90) cc_final: 0.5721 (p90) REVERT: N 34 MET cc_start: 0.8972 (mmm) cc_final: 0.8528 (mmm) REVERT: N 67 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.5015 (ptm-80) REVERT: N 120 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8683 (tp40) REVERT: R 139 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8397 (tt0) REVERT: R 142 LEU cc_start: 0.8272 (tp) cc_final: 0.7904 (tm) REVERT: R 148 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6849 (p90) REVERT: R 202 LYS cc_start: 0.8065 (tmmt) cc_final: 0.7603 (mptt) REVERT: R 260 LEU cc_start: 0.8258 (pt) cc_final: 0.7930 (mm) REVERT: R 262 GLU cc_start: 0.8239 (pt0) cc_final: 0.7579 (pm20) REVERT: R 299 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: R 346 LYS cc_start: 0.7562 (mttt) cc_final: 0.6954 (pttm) REVERT: R 394 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: R 406 ASN cc_start: 0.7708 (t0) cc_final: 0.6720 (t0) REVERT: R 408 GLU cc_start: 0.7906 (mp0) cc_final: 0.7464 (mp0) REVERT: R 412 GLU cc_start: 0.8005 (tp30) cc_final: 0.7766 (tm-30) REVERT: R 414 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5963 (mpt180) outliers start: 38 outliers final: 18 residues processed: 188 average time/residue: 0.6074 time to fit residues: 121.6074 Evaluate side-chains 182 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 394 GLN Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098762 restraints weight = 13136.115| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.83 r_work: 0.3227 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8660 Z= 0.140 Angle : 0.565 7.428 11764 Z= 0.298 Chirality : 0.042 0.188 1325 Planarity : 0.004 0.045 1454 Dihedral : 6.479 59.472 1528 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.92 % Allowed : 26.23 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1019 helix: 1.40 (0.26), residues: 404 sheet: -0.33 (0.36), residues: 210 loop : -0.59 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 105 TYR 0.018 0.002 TYR N 95 PHE 0.050 0.002 PHE N 27 TRP 0.021 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8656) covalent geometry : angle 0.56466 (11758) SS BOND : bond 0.00179 ( 3) SS BOND : angle 1.32783 ( 6) hydrogen bonds : bond 0.03407 ( 419) hydrogen bonds : angle 4.49880 ( 1188) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7665 (t0) cc_final: 0.7144 (t0) REVERT: A 343 ASP cc_start: 0.8480 (m-30) cc_final: 0.8126 (m-30) REVERT: A 370 GLU cc_start: 0.7869 (pm20) cc_final: 0.7505 (pm20) REVERT: B 13 GLN cc_start: 0.8180 (mm110) cc_final: 0.7876 (mm110) REVERT: B 19 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.8179 (ttp80) REVERT: B 38 ASP cc_start: 0.8595 (p0) cc_final: 0.8104 (p0) REVERT: B 57 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8444 (ptpp) REVERT: B 138 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8470 (mt-10) REVERT: B 169 TRP cc_start: 0.9101 (m100) cc_final: 0.8833 (m100) REVERT: B 172 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: B 198 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8858 (mt) REVERT: B 215 GLU cc_start: 0.8255 (mp0) cc_final: 0.7432 (mp0) REVERT: B 226 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7316 (tt0) REVERT: B 228 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: B 243 THR cc_start: 0.8001 (p) cc_final: 0.7686 (p) REVERT: G 20 LYS cc_start: 0.7361 (ttpp) cc_final: 0.7141 (tmmt) REVERT: G 21 MET cc_start: 0.7644 (ttp) cc_final: 0.7069 (ttp) REVERT: G 38 MET cc_start: 0.7938 (ptp) cc_final: 0.7556 (ptp) REVERT: G 42 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7666 (mp0) REVERT: N 3 GLN cc_start: 0.7611 (tp40) cc_final: 0.6939 (tm-30) REVERT: N 31 ASN cc_start: 0.8403 (m-40) cc_final: 0.8067 (t0) REVERT: N 32 TYR cc_start: 0.5947 (p90) cc_final: 0.5711 (p90) REVERT: N 34 MET cc_start: 0.9007 (mmm) cc_final: 0.8564 (mmm) REVERT: N 67 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.5028 (ptm-80) REVERT: N 84 ASN cc_start: 0.8658 (m-40) cc_final: 0.8398 (m-40) REVERT: N 90 ASP cc_start: 0.8666 (m-30) cc_final: 0.8391 (m-30) REVERT: N 120 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8664 (tp40) REVERT: R 139 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8329 (tt0) REVERT: R 148 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6960 (p90) REVERT: R 260 LEU cc_start: 0.8308 (pt) cc_final: 0.7987 (mm) REVERT: R 262 GLU cc_start: 0.8169 (pt0) cc_final: 0.7500 (pm20) REVERT: R 299 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7528 (ttm170) REVERT: R 346 LYS cc_start: 0.7591 (mttt) cc_final: 0.6933 (ptpp) REVERT: R 394 GLN cc_start: 0.8352 (pt0) cc_final: 0.7976 (tt0) REVERT: R 406 ASN cc_start: 0.7692 (t0) cc_final: 0.6690 (t0) REVERT: R 408 GLU cc_start: 0.7971 (mp0) cc_final: 0.7497 (mp0) REVERT: R 412 GLU cc_start: 0.8028 (tp30) cc_final: 0.7794 (tm-30) REVERT: R 414 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5986 (mpt180) outliers start: 35 outliers final: 17 residues processed: 178 average time/residue: 0.5691 time to fit residues: 107.5327 Evaluate side-chains 178 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097904 restraints weight = 13214.793| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.84 r_work: 0.3204 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8660 Z= 0.156 Angle : 0.594 9.424 11764 Z= 0.309 Chirality : 0.042 0.150 1325 Planarity : 0.004 0.054 1454 Dihedral : 6.468 59.219 1528 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.14 % Allowed : 27.35 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.27), residues: 1019 helix: 1.46 (0.26), residues: 399 sheet: -0.34 (0.36), residues: 205 loop : -0.56 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.019 0.002 TYR N 95 PHE 0.050 0.002 PHE N 27 TRP 0.022 0.001 TRP A 277 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8656) covalent geometry : angle 0.59257 (11758) SS BOND : bond 0.00151 ( 3) SS BOND : angle 1.63154 ( 6) hydrogen bonds : bond 0.03445 ( 419) hydrogen bonds : angle 4.52755 ( 1188) Misc. bond : bond 0.00039 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8477 (pp20) cc_final: 0.8274 (pp20) REVERT: A 215 ASP cc_start: 0.7671 (t0) cc_final: 0.7151 (t0) REVERT: A 292 ASN cc_start: 0.8524 (t0) cc_final: 0.8162 (t0) REVERT: A 343 ASP cc_start: 0.8446 (m-30) cc_final: 0.8058 (m-30) REVERT: A 354 ASP cc_start: 0.7999 (p0) cc_final: 0.7692 (m-30) REVERT: A 370 GLU cc_start: 0.7846 (pm20) cc_final: 0.7491 (pm20) REVERT: B 13 GLN cc_start: 0.8177 (mm110) cc_final: 0.7872 (mm110) REVERT: B 19 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8155 (ttp80) REVERT: B 38 ASP cc_start: 0.8599 (p0) cc_final: 0.8126 (p0) REVERT: B 57 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8460 (ptpp) REVERT: B 138 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 169 TRP cc_start: 0.9124 (m100) cc_final: 0.8850 (m100) REVERT: B 172 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: B 198 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (mt) REVERT: B 217 MET cc_start: 0.8909 (ptt) cc_final: 0.8456 (pmm) REVERT: B 243 THR cc_start: 0.8139 (p) cc_final: 0.7809 (p) REVERT: G 20 LYS cc_start: 0.7436 (ttpp) cc_final: 0.7209 (tmmt) REVERT: G 21 MET cc_start: 0.7646 (ttp) cc_final: 0.7004 (ttp) REVERT: G 47 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7181 (mp0) REVERT: N 3 GLN cc_start: 0.7608 (tp40) cc_final: 0.6918 (tm-30) REVERT: N 31 ASN cc_start: 0.8437 (m-40) cc_final: 0.8084 (t0) REVERT: N 32 TYR cc_start: 0.5964 (p90) cc_final: 0.5713 (p90) REVERT: N 34 MET cc_start: 0.9052 (mmm) cc_final: 0.8730 (mmm) REVERT: N 67 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.5026 (ptm-80) REVERT: N 84 ASN cc_start: 0.8780 (m-40) cc_final: 0.8510 (m110) REVERT: N 120 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8657 (tp40) REVERT: R 139 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8352 (tt0) REVERT: R 148 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6897 (p90) REVERT: R 260 LEU cc_start: 0.8333 (pt) cc_final: 0.7994 (mm) REVERT: R 262 GLU cc_start: 0.8211 (pt0) cc_final: 0.7521 (pm20) REVERT: R 299 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7391 (ttm170) REVERT: R 346 LYS cc_start: 0.7593 (mttt) cc_final: 0.6960 (ptpp) REVERT: R 394 GLN cc_start: 0.8351 (pt0) cc_final: 0.7987 (tt0) REVERT: R 406 ASN cc_start: 0.7703 (t0) cc_final: 0.6618 (t0) REVERT: R 408 GLU cc_start: 0.8008 (mp0) cc_final: 0.7515 (mp0) REVERT: R 412 GLU cc_start: 0.8064 (tp30) cc_final: 0.7698 (tm-30) REVERT: R 414 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6061 (mpt180) outliers start: 28 outliers final: 19 residues processed: 176 average time/residue: 0.6025 time to fit residues: 112.5036 Evaluate side-chains 179 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 363 HIS Chi-restraints excluded: chain R residue 414 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097231 restraints weight = 13222.795| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.85 r_work: 0.3195 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8660 Z= 0.165 Angle : 0.615 8.291 11764 Z= 0.322 Chirality : 0.042 0.152 1325 Planarity : 0.004 0.054 1454 Dihedral : 6.471 58.855 1528 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.48 % Allowed : 27.02 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1019 helix: 1.48 (0.26), residues: 398 sheet: -0.46 (0.35), residues: 204 loop : -0.56 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 389 TYR 0.021 0.002 TYR N 32 PHE 0.060 0.002 PHE N 27 TRP 0.023 0.002 TRP A 277 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8656) covalent geometry : angle 0.61385 (11758) SS BOND : bond 0.00137 ( 3) SS BOND : angle 1.62194 ( 6) hydrogen bonds : bond 0.03451 ( 419) hydrogen bonds : angle 4.58826 ( 1188) Misc. bond : bond 0.00045 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.19 seconds wall clock time: 62 minutes 20.34 seconds (3740.34 seconds total)