Starting phenix.real_space_refine on Sat Dec 28 15:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7evm_31329/12_2024/7evm_31329_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evm_31329/12_2024/7evm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7evm_31329/12_2024/7evm_31329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evm_31329/12_2024/7evm_31329.map" model { file = "/net/cci-nas-00/data/ceres_data/7evm_31329/12_2024/7evm_31329_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evm_31329/12_2024/7evm_31329_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.26, per 1000 atoms: 0.62 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: 2.29 Conformation dependent library (CDL) restraints added in 914.5 milliseconds 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: 0.80 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: 2.18 Time building geometry restraints manager: 2.60 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- 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 8656 Z= 0.335 Angle : 0.855 13.151 11758 Z= 0.499 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 : 11.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (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 TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 PHE 0.017 0.002 PHE R 280 TYR 0.028 0.002 TYR R 148 ARG 0.005 0.001 ARG B 129 *********************** 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 : 0.944 Fit side-chains revert: symmetry clash 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: 0.7525 (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: 0.7631 (pm20) 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: 0.7999 (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: 0.7691 (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 292 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7300 (mm-30) 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 423 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6876 (pt0) outliers start: 30 outliers final: 5 residues processed: 301 average time/residue: 1.2518 time to fit residues: 400.0216 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 : 0.920 ------------------------------------------------------------------------------- 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 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN N 35 ASN R 171 HIS ** R 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8656 Z= 0.249 Angle : 0.633 7.652 11758 Z= 0.337 Chirality : 0.045 0.157 1325 Planarity : 0.005 0.085 1454 Dihedral : 8.447 63.755 1557 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.81 % Allowed : 19.51 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1019 helix: -0.02 (0.26), residues: 399 sheet: -0.86 (0.33), residues: 209 loop : -1.03 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 214 HIS 0.008 0.001 HIS A 357 PHE 0.021 0.002 PHE A 273 TYR 0.026 0.002 TYR R 148 ARG 0.006 0.001 ARG A 347 *********************** 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 203 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7460 (ttm-80) REVERT: A 31 GLN cc_start: 0.7951 (tp40) cc_final: 0.7703 (tp-100) REVERT: A 213 GLN cc_start: 0.8741 (tt0) cc_final: 0.8133 (tt0) REVERT: A 215 ASP cc_start: 0.7645 (t0) cc_final: 0.7111 (t0) REVERT: A 294 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7614 (mm110) REVERT: A 325 THR cc_start: 0.8870 (m) cc_final: 0.8568 (p) REVERT: A 339 TYR cc_start: 0.7697 (m-80) cc_final: 0.7476 (m-80) REVERT: A 343 ASP cc_start: 0.7972 (m-30) cc_final: 0.7425 (m-30) REVERT: A 349 SER cc_start: 0.8547 (t) cc_final: 0.7542 (p) REVERT: A 352 SER cc_start: 0.8099 (t) cc_final: 0.6941 (t) REVERT: A 378 ASP cc_start: 0.7149 (m-30) cc_final: 0.6898 (m-30) REVERT: B 38 ASP cc_start: 0.8532 (p0) cc_final: 0.7943 (p0) REVERT: B 44 GLN cc_start: 0.7899 (pt0) cc_final: 0.7611 (pt0) REVERT: B 124 TYR cc_start: 0.8402 (m-80) cc_final: 0.7965 (m-80) REVERT: B 138 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 217 MET cc_start: 0.7486 (ptt) cc_final: 0.7240 (ptt) REVERT: B 228 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: B 243 THR cc_start: 0.7438 (p) cc_final: 0.7011 (p) REVERT: G 21 MET cc_start: 0.6999 (tpt) cc_final: 0.6766 (ttp) REVERT: G 38 MET cc_start: 0.7351 (ptp) cc_final: 0.6975 (ttp) REVERT: G 42 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6863 (mp0) REVERT: N 3 GLN cc_start: 0.7334 (tp40) cc_final: 0.6595 (tm-30) REVERT: N 31 ASN cc_start: 0.8096 (m-40) cc_final: 0.7721 (t0) REVERT: N 35 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8320 (p0) REVERT: N 65 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7642 (ttpt) REVERT: N 77 ASN cc_start: 0.7348 (m-40) cc_final: 0.7075 (p0) REVERT: N 110 VAL cc_start: 0.8661 (m) cc_final: 0.8351 (t) REVERT: N 120 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8409 (tp40) REVERT: R 139 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8355 (tt0) REVERT: R 142 LEU cc_start: 0.8339 (tp) cc_final: 0.8041 (tm) REVERT: R 262 GLU cc_start: 0.8082 (pt0) cc_final: 0.7721 (pt0) REVERT: R 346 LYS cc_start: 0.7514 (mttt) cc_final: 0.6937 (pttm) REVERT: R 394 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: R 397 MET cc_start: 0.7552 (mmt) cc_final: 0.7220 (mmt) REVERT: R 407 ASN cc_start: 0.8956 (m-40) cc_final: 0.8630 (m110) REVERT: R 412 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7687 (tm-30) outliers start: 34 outliers final: 12 residues processed: 193 average time/residue: 1.2146 time to fit residues: 249.3712 Evaluate side-chains 161 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 65 LYS 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 349 LEU 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 50 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 176 GLN B 230 ASN R 171 HIS R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8656 Z= 0.322 Angle : 0.630 7.302 11758 Z= 0.332 Chirality : 0.045 0.149 1325 Planarity : 0.005 0.060 1454 Dihedral : 7.307 59.726 1533 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.60 % Allowed : 21.30 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1019 helix: 0.50 (0.26), residues: 405 sheet: -0.65 (0.33), residues: 215 loop : -1.01 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 277 HIS 0.004 0.001 HIS R 363 PHE 0.032 0.002 PHE N 27 TYR 0.021 0.002 TYR R 148 ARG 0.009 0.001 ARG R 421 *********************** 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 199 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7937 (tp40) cc_final: 0.7668 (tp-100) REVERT: A 213 GLN cc_start: 0.8718 (tt0) cc_final: 0.8104 (tt0) REVERT: A 215 ASP cc_start: 0.7657 (t0) cc_final: 0.7094 (t0) REVERT: A 277 TRP cc_start: 0.7527 (m100) cc_final: 0.7293 (m100) REVERT: A 296 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8651 (tp) REVERT: A 325 THR cc_start: 0.8960 (m) cc_final: 0.8646 (p) REVERT: A 339 TYR cc_start: 0.7797 (m-80) cc_final: 0.7554 (m-80) REVERT: A 343 ASP cc_start: 0.8060 (m-30) cc_final: 0.7586 (m-30) REVERT: B 13 GLN cc_start: 0.8030 (mm110) cc_final: 0.7761 (mm110) REVERT: B 38 ASP cc_start: 0.8502 (p0) cc_final: 0.7925 (p0) REVERT: B 44 GLN cc_start: 0.7950 (pt0) cc_final: 0.7630 (pt0) REVERT: B 138 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 163 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7289 (p0) REVERT: B 172 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: B 226 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7084 (mt-10) REVERT: B 243 THR cc_start: 0.7556 (p) cc_final: 0.7108 (p) REVERT: G 21 MET cc_start: 0.7027 (tpt) cc_final: 0.6796 (ttp) REVERT: G 38 MET cc_start: 0.7473 (ptp) cc_final: 0.7027 (ttp) REVERT: G 42 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7256 (mp0) REVERT: N 3 GLN cc_start: 0.7387 (tp40) cc_final: 0.6749 (tm-30) REVERT: N 31 ASN cc_start: 0.8311 (m-40) cc_final: 0.8023 (t0) REVERT: N 110 VAL cc_start: 0.8603 (m) cc_final: 0.8340 (t) REVERT: N 120 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8364 (tp40) REVERT: R 139 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8358 (tt0) REVERT: R 142 LEU cc_start: 0.8288 (tp) cc_final: 0.8022 (tm) REVERT: R 262 GLU cc_start: 0.8101 (pt0) cc_final: 0.7880 (pt0) REVERT: R 302 ASN cc_start: 0.8940 (t0) cc_final: 0.8571 (t0) REVERT: R 346 LYS cc_start: 0.7579 (mttt) cc_final: 0.6998 (pttm) REVERT: R 394 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: R 397 MET cc_start: 0.7578 (mmt) cc_final: 0.7218 (mmt) REVERT: R 423 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6260 (tm-30) outliers start: 41 outliers final: 17 residues processed: 187 average time/residue: 1.2369 time to fit residues: 246.1174 Evaluate side-chains 165 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 190 LEU 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 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 230 ASN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8656 Z= 0.194 Angle : 0.567 7.223 11758 Z= 0.299 Chirality : 0.042 0.147 1325 Planarity : 0.004 0.046 1454 Dihedral : 6.930 58.000 1531 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.71 % Allowed : 22.42 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1019 helix: 0.95 (0.26), residues: 399 sheet: -0.56 (0.34), residues: 210 loop : -0.88 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.003 0.001 HIS A 362 PHE 0.020 0.001 PHE N 27 TYR 0.020 0.001 TYR R 148 ARG 0.009 0.001 ARG B 214 *********************** 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 204 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7840 (mpt) cc_final: 0.7086 (mpt) REVERT: A 213 GLN cc_start: 0.8686 (tt0) cc_final: 0.8051 (tt0) REVERT: A 215 ASP cc_start: 0.7507 (t0) cc_final: 0.6960 (t0) REVERT: A 325 THR cc_start: 0.8957 (m) cc_final: 0.8658 (p) REVERT: A 343 ASP cc_start: 0.8037 (m-30) cc_final: 0.7671 (m-30) REVERT: A 370 GLU cc_start: 0.7790 (pm20) cc_final: 0.7491 (pm20) REVERT: B 13 GLN cc_start: 0.8096 (mm110) cc_final: 0.7836 (mm110) REVERT: B 38 ASP cc_start: 0.8505 (p0) cc_final: 0.7951 (p0) REVERT: B 44 GLN cc_start: 0.8029 (pt0) cc_final: 0.7672 (pt0) REVERT: B 57 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8573 (ptpp) REVERT: B 138 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 172 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 214 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7834 (mtm110) REVERT: B 215 GLU cc_start: 0.7806 (mp0) cc_final: 0.7199 (mp0) REVERT: B 226 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7101 (mt-10) REVERT: B 243 THR cc_start: 0.7587 (p) cc_final: 0.7146 (p) REVERT: G 38 MET cc_start: 0.7498 (ptp) cc_final: 0.7032 (ttp) REVERT: G 42 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7246 (mp0) REVERT: G 47 GLU cc_start: 0.7285 (mp0) cc_final: 0.6992 (mp0) REVERT: N 3 GLN cc_start: 0.7360 (tp40) cc_final: 0.6724 (tm-30) REVERT: N 31 ASN cc_start: 0.8192 (m-40) cc_final: 0.7822 (t0) REVERT: N 67 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.4384 (ptm-80) REVERT: N 105 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7431 (ttm110) REVERT: N 110 VAL cc_start: 0.8692 (m) cc_final: 0.8442 (t) REVERT: N 120 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8339 (tp40) REVERT: R 139 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8408 (tt0) REVERT: R 142 LEU cc_start: 0.8272 (tp) cc_final: 0.8018 (tm) REVERT: R 148 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6526 (p90) REVERT: R 203 TRP cc_start: 0.7147 (t-100) cc_final: 0.6930 (t-100) REVERT: R 260 LEU cc_start: 0.7939 (pt) cc_final: 0.7717 (mm) REVERT: R 346 LYS cc_start: 0.7538 (mttt) cc_final: 0.6967 (pttm) REVERT: R 394 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: R 412 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: R 423 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6173 (tm-30) outliers start: 42 outliers final: 15 residues processed: 192 average time/residue: 1.1857 time to fit residues: 242.9419 Evaluate side-chains 175 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 335 THR 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 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 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 412 GLU 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 55 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8656 Z= 0.198 Angle : 0.568 7.302 11758 Z= 0.293 Chirality : 0.042 0.166 1325 Planarity : 0.004 0.043 1454 Dihedral : 6.799 58.286 1531 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.48 % Allowed : 24.10 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1019 helix: 1.16 (0.26), residues: 399 sheet: -0.55 (0.34), residues: 216 loop : -0.81 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.004 0.001 HIS R 363 PHE 0.023 0.001 PHE R 385 TYR 0.018 0.001 TYR R 148 ARG 0.010 0.001 ARG B 19 *********************** 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 188 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8703 (tt0) cc_final: 0.8048 (tt0) REVERT: A 215 ASP cc_start: 0.7497 (t0) cc_final: 0.6950 (t0) REVERT: A 317 ARG cc_start: 0.7976 (ptp-110) cc_final: 0.7662 (ptp90) REVERT: A 325 THR cc_start: 0.8924 (m) cc_final: 0.8662 (p) REVERT: A 343 ASP cc_start: 0.8044 (m-30) cc_final: 0.7636 (m-30) REVERT: A 370 GLU cc_start: 0.7785 (pm20) cc_final: 0.7531 (pm20) REVERT: B 13 GLN cc_start: 0.8100 (mm110) cc_final: 0.7838 (mm110) REVERT: B 38 ASP cc_start: 0.8607 (p0) cc_final: 0.8062 (p0) REVERT: B 57 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8585 (ptpp) REVERT: B 138 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 169 TRP cc_start: 0.8895 (m100) cc_final: 0.8594 (m100) REVERT: B 172 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 214 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7780 (mtm110) REVERT: B 215 GLU cc_start: 0.7850 (mp0) cc_final: 0.7154 (mp0) REVERT: B 226 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7027 (mt-10) REVERT: B 228 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: B 243 THR cc_start: 0.7564 (p) cc_final: 0.7105 (p) REVERT: G 20 LYS cc_start: 0.7130 (tmmt) cc_final: 0.6825 (ttpp) REVERT: G 21 MET cc_start: 0.7240 (ttp) cc_final: 0.6520 (ttp) REVERT: G 38 MET cc_start: 0.7411 (ptp) cc_final: 0.5553 (ttp) REVERT: G 42 GLU cc_start: 0.7855 (mt-10) cc_final: 0.6953 (mp0) REVERT: G 47 GLU cc_start: 0.7272 (mp0) cc_final: 0.7051 (mp0) REVERT: N 3 GLN cc_start: 0.7350 (tp40) cc_final: 0.6745 (tm-30) REVERT: N 31 ASN cc_start: 0.8178 (m-40) cc_final: 0.7801 (t0) REVERT: N 120 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8344 (tp40) REVERT: R 139 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8419 (tt0) REVERT: R 142 LEU cc_start: 0.8321 (tp) cc_final: 0.8090 (tm) REVERT: R 148 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6620 (p90) REVERT: R 203 TRP cc_start: 0.7267 (t-100) cc_final: 0.7029 (t-100) REVERT: R 260 LEU cc_start: 0.7970 (pt) cc_final: 0.7728 (mm) REVERT: R 302 ASN cc_start: 0.8814 (t0) cc_final: 0.8501 (t0) REVERT: R 346 LYS cc_start: 0.7532 (mttt) cc_final: 0.6961 (pttm) REVERT: R 394 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7819 (tt0) outliers start: 31 outliers final: 17 residues processed: 179 average time/residue: 1.1903 time to fit residues: 227.1342 Evaluate side-chains 179 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 228 ASP 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 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 282 VAL Chi-restraints excluded: chain R residue 394 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0670 chunk 19 optimal weight: 0.0970 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN N 1 GLN R 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8656 Z= 0.200 Angle : 0.552 8.211 11758 Z= 0.288 Chirality : 0.041 0.143 1325 Planarity : 0.004 0.042 1454 Dihedral : 6.614 58.444 1528 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.26 % Allowed : 24.22 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 1019 helix: 1.22 (0.26), residues: 406 sheet: -0.48 (0.35), residues: 212 loop : -0.81 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.004 0.001 HIS R 363 PHE 0.016 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.009 0.001 ARG B 19 *********************** 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 200 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8701 (tt0) cc_final: 0.8092 (tt0) REVERT: A 215 ASP cc_start: 0.7495 (t0) cc_final: 0.6966 (t0) REVERT: A 317 ARG cc_start: 0.7891 (ptp-110) cc_final: 0.7587 (ptp90) REVERT: A 325 THR cc_start: 0.8956 (m) cc_final: 0.8720 (p) REVERT: A 343 ASP cc_start: 0.8037 (m-30) cc_final: 0.7616 (m-30) REVERT: A 370 GLU cc_start: 0.7711 (pm20) cc_final: 0.7434 (pm20) REVERT: B 13 GLN cc_start: 0.8100 (mm110) cc_final: 0.7818 (mm110) REVERT: B 38 ASP cc_start: 0.8588 (p0) cc_final: 0.8078 (p0) REVERT: B 57 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8590 (ptpp) REVERT: B 138 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 169 TRP cc_start: 0.8908 (m100) cc_final: 0.8622 (m100) REVERT: B 172 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 215 GLU cc_start: 0.7886 (mp0) cc_final: 0.7202 (mp0) REVERT: B 226 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 228 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: B 243 THR cc_start: 0.7593 (p) cc_final: 0.7141 (p) REVERT: G 21 MET cc_start: 0.7246 (ttp) cc_final: 0.6623 (ttp) REVERT: G 38 MET cc_start: 0.7471 (ptp) cc_final: 0.5577 (ttp) REVERT: G 42 GLU cc_start: 0.7906 (mt-10) cc_final: 0.6986 (mp0) REVERT: N 3 GLN cc_start: 0.7364 (tp40) cc_final: 0.6645 (tm-30) REVERT: N 31 ASN cc_start: 0.8165 (m-40) cc_final: 0.7804 (t0) REVERT: N 120 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8270 (tp40) REVERT: R 139 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8401 (tt0) REVERT: R 142 LEU cc_start: 0.8316 (tp) cc_final: 0.8061 (tm) REVERT: R 146 ILE cc_start: 0.6564 (tt) cc_final: 0.6249 (tp) REVERT: R 148 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6706 (p90) REVERT: R 203 TRP cc_start: 0.7248 (t-100) cc_final: 0.6982 (t-100) REVERT: R 262 GLU cc_start: 0.8086 (pt0) cc_final: 0.7730 (pm20) REVERT: R 346 LYS cc_start: 0.7509 (mttt) cc_final: 0.6956 (pttm) REVERT: R 388 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7902 (mt) REVERT: R 394 GLN cc_start: 0.8255 (pt0) cc_final: 0.7884 (tt0) outliers start: 38 outliers final: 23 residues processed: 188 average time/residue: 1.1569 time to fit residues: 232.5932 Evaluate side-chains 180 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS 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 228 ASP 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 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 282 VAL Chi-restraints excluded: chain R residue 388 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8656 Z= 0.241 Angle : 0.577 7.368 11758 Z= 0.303 Chirality : 0.042 0.153 1325 Planarity : 0.004 0.051 1454 Dihedral : 6.607 57.118 1528 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.71 % Allowed : 25.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 1019 helix: 1.27 (0.26), residues: 406 sheet: -0.51 (0.35), residues: 216 loop : -0.69 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 277 HIS 0.003 0.001 HIS B 225 PHE 0.024 0.001 PHE R 385 TYR 0.024 0.002 TYR R 305 ARG 0.012 0.001 ARG N 105 *********************** 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 204 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8264 (pp20) cc_final: 0.8030 (pp20) REVERT: A 215 ASP cc_start: 0.7512 (t0) cc_final: 0.6972 (t0) REVERT: A 317 ARG cc_start: 0.7956 (ptp-110) cc_final: 0.7672 (ptp90) REVERT: A 325 THR cc_start: 0.8956 (m) cc_final: 0.8748 (p) REVERT: A 343 ASP cc_start: 0.8061 (m-30) cc_final: 0.7626 (m-30) REVERT: A 370 GLU cc_start: 0.7638 (pm20) cc_final: 0.7289 (pm20) REVERT: B 13 GLN cc_start: 0.8116 (mm110) cc_final: 0.7834 (mm110) REVERT: B 38 ASP cc_start: 0.8580 (p0) cc_final: 0.8076 (p0) REVERT: B 57 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8608 (ptpp) REVERT: B 138 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 169 TRP cc_start: 0.8920 (m100) cc_final: 0.8626 (m100) REVERT: B 172 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 215 GLU cc_start: 0.7779 (mp0) cc_final: 0.7411 (mp0) REVERT: B 226 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7374 (mt-10) REVERT: B 228 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: B 243 THR cc_start: 0.7568 (p) cc_final: 0.7110 (p) REVERT: G 21 MET cc_start: 0.7312 (ttp) cc_final: 0.6803 (ttp) REVERT: G 38 MET cc_start: 0.7564 (ptp) cc_final: 0.5593 (ttp) REVERT: G 42 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7029 (mp0) REVERT: N 3 GLN cc_start: 0.7313 (tp40) cc_final: 0.6618 (tm-30) REVERT: N 31 ASN cc_start: 0.8186 (m-40) cc_final: 0.7814 (t0) REVERT: N 34 MET cc_start: 0.8774 (mmm) cc_final: 0.8137 (mmm) REVERT: R 142 LEU cc_start: 0.8303 (tp) cc_final: 0.8053 (tm) REVERT: R 146 ILE cc_start: 0.6793 (tt) cc_final: 0.6510 (tp) REVERT: R 148 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6647 (p90) REVERT: R 203 TRP cc_start: 0.7296 (t-100) cc_final: 0.7002 (t-100) REVERT: R 262 GLU cc_start: 0.8101 (pt0) cc_final: 0.7672 (pm20) REVERT: R 346 LYS cc_start: 0.7526 (mttt) cc_final: 0.6953 (pttm) REVERT: R 388 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7935 (mm) REVERT: R 394 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: R 406 ASN cc_start: 0.7804 (t0) cc_final: 0.6730 (t0) REVERT: R 408 GLU cc_start: 0.7695 (mp0) cc_final: 0.7311 (mp0) REVERT: R 414 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.5993 (mpt180) outliers start: 42 outliers final: 23 residues processed: 188 average time/residue: 1.1156 time to fit residues: 224.7695 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 : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS 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 228 ASP Chi-restraints excluded: chain B residue 249 THR 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 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 388 LEU 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 29 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8656 Z= 0.280 Angle : 0.620 11.440 11758 Z= 0.318 Chirality : 0.043 0.145 1325 Planarity : 0.004 0.045 1454 Dihedral : 6.624 56.138 1528 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.37 % Allowed : 25.56 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 1019 helix: 1.24 (0.26), residues: 407 sheet: -0.50 (0.35), residues: 214 loop : -0.57 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 277 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE A 212 TYR 0.020 0.002 TYR N 95 ARG 0.013 0.001 ARG B 19 *********************** 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 197 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7501 (t0) cc_final: 0.6965 (t0) REVERT: A 317 ARG cc_start: 0.7939 (ptp-110) cc_final: 0.7653 (ptp90) REVERT: A 325 THR cc_start: 0.8987 (m) cc_final: 0.8778 (p) REVERT: A 343 ASP cc_start: 0.8064 (m-30) cc_final: 0.7622 (m-30) REVERT: A 370 GLU cc_start: 0.7613 (pm20) cc_final: 0.7230 (pm20) REVERT: B 13 GLN cc_start: 0.8129 (mm110) cc_final: 0.7862 (mm110) REVERT: B 38 ASP cc_start: 0.8585 (p0) cc_final: 0.8111 (p0) REVERT: B 138 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 172 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 198 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 215 GLU cc_start: 0.7899 (mp0) cc_final: 0.7078 (mp0) REVERT: B 226 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7436 (mt-10) REVERT: B 228 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 243 THR cc_start: 0.7565 (p) cc_final: 0.7103 (p) REVERT: G 21 MET cc_start: 0.7338 (ttp) cc_final: 0.6596 (ttp) REVERT: G 38 MET cc_start: 0.7774 (ptp) cc_final: 0.6151 (ptp) REVERT: G 42 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7069 (mp0) REVERT: N 3 GLN cc_start: 0.7281 (tp40) cc_final: 0.6608 (tm-30) REVERT: N 31 ASN cc_start: 0.8207 (m-40) cc_final: 0.7821 (t0) REVERT: N 34 MET cc_start: 0.8741 (mmm) cc_final: 0.8341 (mmm) REVERT: N 117 TYR cc_start: 0.7650 (m-80) cc_final: 0.7390 (m-80) REVERT: N 120 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8326 (tp40) REVERT: R 142 LEU cc_start: 0.8277 (tp) cc_final: 0.7910 (tm) REVERT: R 148 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6781 (p90) REVERT: R 202 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7707 (mptt) REVERT: R 203 TRP cc_start: 0.7325 (t-100) cc_final: 0.6464 (t-100) REVERT: R 299 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: R 346 LYS cc_start: 0.7561 (mttt) cc_final: 0.6943 (ptpp) REVERT: R 394 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: R 406 ASN cc_start: 0.7970 (t0) cc_final: 0.6913 (t160) REVERT: R 408 GLU cc_start: 0.7688 (mp0) cc_final: 0.7235 (mp0) outliers start: 39 outliers final: 25 residues processed: 182 average time/residue: 1.2298 time to fit residues: 238.1702 Evaluate side-chains 182 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS 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 349 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 163 ASP 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 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 63 SER 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 281 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 363 HIS 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 90 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8656 Z= 0.247 Angle : 0.625 9.429 11758 Z= 0.323 Chirality : 0.043 0.225 1325 Planarity : 0.005 0.060 1454 Dihedral : 6.584 55.263 1528 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.92 % Allowed : 27.24 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 1019 helix: 1.21 (0.26), residues: 407 sheet: -0.53 (0.35), residues: 208 loop : -0.52 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 277 HIS 0.004 0.001 HIS B 225 PHE 0.028 0.002 PHE R 169 TYR 0.020 0.002 TYR N 95 ARG 0.014 0.001 ARG A 389 *********************** 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 191 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7492 (t0) cc_final: 0.6951 (t0) REVERT: A 317 ARG cc_start: 0.7937 (ptp-110) cc_final: 0.7644 (ptp90) REVERT: A 325 THR cc_start: 0.8982 (m) cc_final: 0.8780 (p) REVERT: A 343 ASP cc_start: 0.8064 (m-30) cc_final: 0.7621 (m-30) REVERT: A 370 GLU cc_start: 0.7599 (pm20) cc_final: 0.7224 (pm20) REVERT: A 392 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: B 13 GLN cc_start: 0.8112 (mm110) cc_final: 0.7848 (mm110) REVERT: B 38 ASP cc_start: 0.8576 (p0) cc_final: 0.8098 (p0) REVERT: B 138 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 172 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: B 198 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8615 (mt) REVERT: B 215 GLU cc_start: 0.7823 (mp0) cc_final: 0.7486 (mp0) REVERT: B 217 MET cc_start: 0.8464 (ptt) cc_final: 0.8037 (pmm) REVERT: B 226 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7422 (mt-10) REVERT: B 228 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: B 243 THR cc_start: 0.7562 (p) cc_final: 0.7104 (p) REVERT: G 21 MET cc_start: 0.7359 (ttp) cc_final: 0.6519 (ttp) REVERT: G 38 MET cc_start: 0.7783 (ptp) cc_final: 0.6171 (ptp) REVERT: G 42 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7046 (mp0) REVERT: G 47 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6905 (mp0) REVERT: N 3 GLN cc_start: 0.7276 (tp40) cc_final: 0.6607 (tm-30) REVERT: N 31 ASN cc_start: 0.8195 (m-40) cc_final: 0.7827 (t0) REVERT: N 34 MET cc_start: 0.8748 (mmm) cc_final: 0.8380 (mmm) REVERT: N 67 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.4104 (ptm-80) REVERT: N 84 ASN cc_start: 0.8277 (m-40) cc_final: 0.8005 (m-40) REVERT: N 90 ASP cc_start: 0.8194 (m-30) cc_final: 0.7984 (m-30) REVERT: N 120 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8342 (tp40) REVERT: R 142 LEU cc_start: 0.8300 (tp) cc_final: 0.8052 (tm) REVERT: R 148 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6670 (p90) REVERT: R 202 LYS cc_start: 0.8219 (tmmt) cc_final: 0.7684 (mptt) REVERT: R 203 TRP cc_start: 0.7334 (t-100) cc_final: 0.6482 (t-100) REVERT: R 262 GLU cc_start: 0.8259 (pt0) cc_final: 0.7799 (pm20) REVERT: R 299 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: R 346 LYS cc_start: 0.7545 (mttt) cc_final: 0.6962 (pttm) REVERT: R 388 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7899 (mm) REVERT: R 394 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: R 406 ASN cc_start: 0.8017 (t0) cc_final: 0.6958 (t0) REVERT: R 408 GLU cc_start: 0.7741 (mp0) cc_final: 0.7326 (mp0) outliers start: 35 outliers final: 22 residues processed: 179 average time/residue: 1.2592 time to fit residues: 239.9921 Evaluate side-chains 181 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS 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 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 392 GLU 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 163 ASP 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 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 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 281 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 GLN 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 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS R 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8656 Z= 0.241 Angle : 0.622 8.521 11758 Z= 0.323 Chirality : 0.043 0.216 1325 Planarity : 0.004 0.055 1454 Dihedral : 6.558 54.266 1528 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.92 % Allowed : 27.35 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 1019 helix: 1.20 (0.26), residues: 407 sheet: -0.52 (0.35), residues: 208 loop : -0.49 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 306 HIS 0.003 0.001 HIS B 225 PHE 0.015 0.001 PHE A 212 TYR 0.020 0.002 TYR N 95 ARG 0.013 0.001 ARG A 389 ********************** 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 191 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8442 (pp20) cc_final: 0.8229 (pp20) REVERT: A 215 ASP cc_start: 0.7486 (t0) cc_final: 0.6945 (t0) REVERT: A 317 ARG cc_start: 0.7934 (ptp-110) cc_final: 0.7639 (ptp90) REVERT: A 343 ASP cc_start: 0.8070 (m-30) cc_final: 0.7626 (m-30) REVERT: A 370 GLU cc_start: 0.7578 (pm20) cc_final: 0.7245 (mp0) REVERT: A 392 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: B 13 GLN cc_start: 0.8078 (mm110) cc_final: 0.7811 (mm110) REVERT: B 57 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8575 (ptpp) REVERT: B 138 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 169 TRP cc_start: 0.8939 (m100) cc_final: 0.8638 (m100) REVERT: B 172 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 198 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8608 (mt) REVERT: B 215 GLU cc_start: 0.7964 (mp0) cc_final: 0.7066 (mp0) REVERT: B 217 MET cc_start: 0.8453 (ptt) cc_final: 0.8062 (pmm) REVERT: B 226 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7416 (mt-10) REVERT: B 228 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: B 243 THR cc_start: 0.7556 (p) cc_final: 0.7085 (p) REVERT: G 21 MET cc_start: 0.7312 (ttp) cc_final: 0.6521 (ttp) REVERT: G 47 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6920 (mp0) REVERT: N 3 GLN cc_start: 0.7270 (tp40) cc_final: 0.6601 (tm-30) REVERT: N 31 ASN cc_start: 0.8188 (m-40) cc_final: 0.7812 (t0) REVERT: N 34 MET cc_start: 0.8788 (mmm) cc_final: 0.8250 (mmm) REVERT: N 67 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.4109 (ptm-80) REVERT: N 84 ASN cc_start: 0.8324 (m-40) cc_final: 0.8056 (m-40) REVERT: N 90 ASP cc_start: 0.8111 (m-30) cc_final: 0.7897 (m-30) REVERT: N 120 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8340 (tp40) REVERT: R 142 LEU cc_start: 0.8388 (tp) cc_final: 0.8187 (tm) REVERT: R 148 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6698 (p90) REVERT: R 203 TRP cc_start: 0.7313 (t-100) cc_final: 0.6943 (t-100) REVERT: R 262 GLU cc_start: 0.8271 (pt0) cc_final: 0.7796 (pm20) REVERT: R 299 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: R 320 ASN cc_start: 0.8264 (t0) cc_final: 0.8017 (t0) REVERT: R 346 LYS cc_start: 0.7537 (mttt) cc_final: 0.6891 (ptpp) REVERT: R 388 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7849 (mm) REVERT: R 394 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: R 406 ASN cc_start: 0.8063 (t0) cc_final: 0.6948 (t0) REVERT: R 408 GLU cc_start: 0.7766 (mp0) cc_final: 0.7341 (mp0) REVERT: R 418 GLU cc_start: 0.6468 (pp20) cc_final: 0.6227 (pp20) outliers start: 35 outliers final: 21 residues processed: 179 average time/residue: 1.2308 time to fit residues: 234.2680 Evaluate side-chains 185 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS 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 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 392 GLU 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 163 ASP 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 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 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 281 VAL Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 394 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.0870 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 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 = 0.3787 r_free = 0.3787 target = 0.131640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097998 restraints weight = 13184.605| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.80 r_work: 0.3209 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8656 Z= 0.208 Angle : 0.612 8.245 11758 Z= 0.319 Chirality : 0.042 0.212 1325 Planarity : 0.005 0.055 1454 Dihedral : 6.502 53.562 1528 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.48 % Allowed : 27.91 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 1019 helix: 1.16 (0.26), residues: 407 sheet: -0.47 (0.36), residues: 204 loop : -0.43 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 306 HIS 0.004 0.001 HIS R 180 PHE 0.025 0.001 PHE R 385 TYR 0.019 0.002 TYR N 95 ARG 0.014 0.001 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4121.15 seconds wall clock time: 74 minutes 12.28 seconds (4452.28 seconds total)