Starting phenix.real_space_refine on Fri Aug 22 23:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhi_36266/08_2025/8jhi_36266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhi_36266/08_2025/8jhi_36266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhi_36266/08_2025/8jhi_36266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhi_36266/08_2025/8jhi_36266.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhi_36266/08_2025/8jhi_36266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhi_36266/08_2025/8jhi_36266.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5454 2.51 5 N 1479 2.21 5 O 1566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8562 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1953 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 962 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2619 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 322, 2614 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "C" Number of residues, atoms: 322, 2614 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2680 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BALA R 392 " occ=0.33 ... (8 atoms not shown) pdb=" CB CALA R 392 " occ=0.67 Time building chain proxies: 2.87, per 1000 atoms: 0.34 Number of scatterers: 8562 At special positions: 0 Unit cell: (78.208, 98.176, 151.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1566 8.00 N 1479 7.00 C 5454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 45 " - pdb=" SG CYS N 119 " distance=2.03 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 130 " distance=2.03 Simple disulfide: pdb=" SG CYS R 165 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS R 286 " - pdb=" SG CYS R 361 " distance=2.04 Simple disulfide: pdb=" SG CYS R 458 " - pdb=" SG CYS R 465 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 459.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 38.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 1 through 35 removed outlier: 4.146A pdb=" N MET A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 253 through 278 removed outlier: 4.100A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.539A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.790A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.908A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.687A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.550A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'N' and resid 51 through 55 removed outlier: 3.757A pdb=" N TYR N 55 " --> pdb=" O PHE N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 88 removed outlier: 3.514A pdb=" N LYS N 88 " --> pdb=" O GLY N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 88' Processing helix chain 'N' and resid 110 through 114 removed outlier: 3.677A pdb=" N THR N 114 " --> pdb=" O PRO N 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 225 removed outlier: 4.313A pdb=" N ILE R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER R 215 " --> pdb=" O ILE R 211 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR R 217 " --> pdb=" O CYS R 213 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 236 Processing helix chain 'R' and resid 237 through 264 removed outlier: 3.941A pdb=" N VAL R 248 " --> pdb=" O CYS R 244 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 292 removed outlier: 3.909A pdb=" N THR R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET R 288 " --> pdb=" O LYS R 284 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 316 Processing helix chain 'R' and resid 324 through 326 No H-bonds generated for 'chain 'R' and resid 324 through 326' Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 336 through 341 Processing helix chain 'R' and resid 344 through 348 Processing helix chain 'R' and resid 375 through 408 removed outlier: 3.808A pdb=" N VAL R 400 " --> pdb=" O SER R 396 " (cutoff:3.500A) Proline residue: R 405 - end of helix Processing helix chain 'R' and resid 413 through 457 Proline residue: R 431 - end of helix removed outlier: 5.363A pdb=" N GLY R 447 " --> pdb=" O GLN R 443 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE R 448 " --> pdb=" O ALA R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 476 through 490 removed outlier: 3.512A pdb=" N PHE R 480 " --> pdb=" O ASP R 476 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 497 removed outlier: 3.772A pdb=" N PHE R 496 " --> pdb=" O ILE R 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.243A pdb=" N HIS A 36 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE A 222 " --> pdb=" O HIS A 36 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 38 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG A 37 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE A 245 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 39 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 247 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 41 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.505A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.913A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.128A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.940A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.710A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.664A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 26 through 30 Processing sheet with id=AB1, first strand: chain 'N' and resid 81 through 83 removed outlier: 3.669A pdb=" N SER N 82 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP N 70 " --> pdb=" O ARG N 61 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG N 61 " --> pdb=" O TRP N 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 352 through 354 376 hydrogen bonds defined for protein. 1054 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2782 1.35 - 1.48: 2214 1.48 - 1.60: 3659 1.60 - 1.73: 0 1.73 - 1.86: 90 Bond restraints: 8745 Sorted by residual: bond pdb=" C ARG R 236 " pdb=" N PRO R 237 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.47e+00 bond pdb=" CB ILE R 292 " pdb=" CG1 ILE R 292 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" CA ILE R 292 " pdb=" CB ILE R 292 " ideal model delta sigma weight residual 1.540 1.583 -0.043 2.70e-02 1.37e+03 2.48e+00 bond pdb=" CB CYS R 286 " pdb=" SG CYS R 286 " ideal model delta sigma weight residual 1.808 1.856 -0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB CYS N 122 " pdb=" SG CYS N 122 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 8740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11476 1.79 - 3.57: 298 3.57 - 5.36: 36 5.36 - 7.14: 20 7.14 - 8.93: 4 Bond angle restraints: 11834 Sorted by residual: angle pdb=" CA CYS R 286 " pdb=" CB CYS R 286 " pdb=" SG CYS R 286 " ideal model delta sigma weight residual 114.40 123.33 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" C LEU R 258 " pdb=" N GLU R 259 " pdb=" CA GLU R 259 " ideal model delta sigma weight residual 121.76 128.43 -6.67 2.19e+00 2.09e-01 9.27e+00 angle pdb=" C TYR R 461 " pdb=" N HIS R 462 " pdb=" CA HIS R 462 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.24e+00 angle pdb=" C LYS R 408 " pdb=" N GLU R 409 " pdb=" CA GLU R 409 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.42e+00 angle pdb=" N GLU B 10 " pdb=" CA GLU B 10 " pdb=" CB GLU B 10 " ideal model delta sigma weight residual 110.39 115.19 -4.80 1.66e+00 3.63e-01 8.35e+00 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4684 17.77 - 35.55: 439 35.55 - 53.32: 74 53.32 - 71.09: 15 71.09 - 88.87: 9 Dihedral angle restraints: 5221 sinusoidal: 2094 harmonic: 3127 Sorted by residual: dihedral pdb=" CB CYS N 122 " pdb=" SG CYS N 122 " pdb=" SG CYS N 130 " pdb=" CB CYS N 130 " ideal model delta sinusoidal sigma weight residual -86.00 -140.41 54.41 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CB CYS R 165 " pdb=" SG CYS R 165 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual -86.00 -137.85 51.85 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CA SER R 215 " pdb=" C SER R 215 " pdb=" N ALA R 216 " pdb=" CA ALA R 216 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 823 0.037 - 0.074: 361 0.074 - 0.110: 100 0.110 - 0.147: 28 0.147 - 0.184: 5 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA TYR R 233 " pdb=" N TYR R 233 " pdb=" C TYR R 233 " pdb=" CB TYR R 233 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1314 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 121 " 0.194 9.50e-02 1.11e+02 8.70e-02 4.70e+00 pdb=" NE ARG N 121 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG N 121 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG N 121 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 463 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO R 464 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 464 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 464 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 140 " 0.014 2.00e-02 2.50e+03 1.51e-02 4.54e+00 pdb=" CG TYR N 140 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR N 140 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR N 140 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR N 140 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR N 140 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR N 140 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 140 " -0.001 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 271 2.71 - 3.26: 8446 3.26 - 3.80: 14003 3.80 - 4.35: 17259 4.35 - 4.90: 28633 Nonbonded interactions: 68612 Sorted by model distance: nonbonded pdb=" OH TYR R 241 " pdb=" O VAL R 490 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.248 3.040 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 121 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.285 3.040 ... (remaining 68607 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=0.33 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: 2.060 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8751 Z= 0.166 Angle : 0.711 8.929 11846 Z= 0.364 Chirality : 0.045 0.184 1317 Planarity : 0.006 0.087 1505 Dihedral : 14.305 88.867 3185 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.25), residues: 1060 helix: 0.24 (0.27), residues: 361 sheet: 0.14 (0.35), residues: 219 loop : -1.55 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 457 TYR 0.037 0.002 TYR N 140 PHE 0.019 0.002 PHE R 480 TRP 0.017 0.001 TRP R 453 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8745) covalent geometry : angle 0.70653 (11834) SS BOND : bond 0.00272 ( 6) SS BOND : angle 2.62952 ( 12) hydrogen bonds : bond 0.13107 ( 376) hydrogen bonds : angle 5.52726 ( 1054) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.8762 (m-10) cc_final: 0.8512 (m-10) REVERT: B 292 PHE cc_start: 0.8266 (m-10) cc_final: 0.7893 (m-10) REVERT: C 41 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8419 (tm-30) REVERT: R 192 MET cc_start: 0.6198 (pmm) cc_final: 0.5666 (pmm) REVERT: R 298 MET cc_start: 0.7031 (mmp) cc_final: 0.6673 (mmm) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1234 time to fit residues: 37.7750 Evaluate side-chains 171 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 13 GLN B 220 GLN B 340 ASN N 105 GLN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.160926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119887 restraints weight = 13662.362| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.61 r_work: 0.3458 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8751 Z= 0.149 Angle : 0.630 7.167 11846 Z= 0.325 Chirality : 0.043 0.167 1317 Planarity : 0.005 0.050 1505 Dihedral : 4.611 30.869 1183 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.48 % Allowed : 11.87 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1060 helix: 0.84 (0.29), residues: 359 sheet: 0.15 (0.36), residues: 213 loop : -1.38 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 457 TYR 0.020 0.002 TYR R 241 PHE 0.043 0.002 PHE R 219 TRP 0.013 0.001 TRP R 453 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8745) covalent geometry : angle 0.62812 (11834) SS BOND : bond 0.00141 ( 6) SS BOND : angle 1.77180 ( 12) hydrogen bonds : bond 0.04059 ( 376) hydrogen bonds : angle 4.64216 ( 1054) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 213 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: B 61 MET cc_start: 0.8890 (ppp) cc_final: 0.8403 (ppp) REVERT: B 111 TYR cc_start: 0.9153 (m-10) cc_final: 0.8852 (m-10) REVERT: B 262 MET cc_start: 0.8168 (tpp) cc_final: 0.7491 (tpp) REVERT: B 292 PHE cc_start: 0.8713 (m-10) cc_final: 0.8508 (m-10) REVERT: C 41 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 51 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6598 (mtm180) REVERT: R 298 MET cc_start: 0.7852 (mmp) cc_final: 0.7514 (mmm) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.0847 time to fit residues: 21.7875 Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 110 ASN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.154507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112855 restraints weight = 13617.886| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.54 r_work: 0.3407 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8751 Z= 0.188 Angle : 0.636 8.758 11846 Z= 0.327 Chirality : 0.044 0.158 1317 Planarity : 0.004 0.050 1505 Dihedral : 4.571 30.618 1183 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.13 % Allowed : 14.13 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.27), residues: 1060 helix: 1.06 (0.29), residues: 359 sheet: 0.17 (0.37), residues: 204 loop : -1.33 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.022 0.002 TYR R 241 PHE 0.029 0.002 PHE R 219 TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8745) covalent geometry : angle 0.63372 (11834) SS BOND : bond 0.00147 ( 6) SS BOND : angle 1.84235 ( 12) hydrogen bonds : bond 0.03862 ( 376) hydrogen bonds : angle 4.47648 ( 1054) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8349 (mm-30) REVERT: A 213 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8708 (tp40) REVERT: A 220 HIS cc_start: 0.7993 (m-70) cc_final: 0.7695 (m-70) REVERT: B 61 MET cc_start: 0.9037 (ppp) cc_final: 0.8531 (ppp) REVERT: B 262 MET cc_start: 0.8227 (tpp) cc_final: 0.7563 (tpp) REVERT: B 289 TYR cc_start: 0.9167 (m-80) cc_final: 0.8927 (m-80) REVERT: C 41 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8335 (tm-30) REVERT: C 51 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7172 (mtm180) REVERT: N 112 GLU cc_start: 0.8580 (pm20) cc_final: 0.8311 (pm20) REVERT: R 219 PHE cc_start: 0.6303 (m-80) cc_final: 0.6102 (m-80) outliers start: 29 outliers final: 24 residues processed: 192 average time/residue: 0.0818 time to fit residues: 21.3637 Evaluate side-chains 199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 25 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN N 58 ASN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114744 restraints weight = 13672.030| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.58 r_work: 0.3450 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8751 Z= 0.119 Angle : 0.596 8.121 11846 Z= 0.301 Chirality : 0.042 0.153 1317 Planarity : 0.004 0.049 1505 Dihedral : 4.438 29.645 1183 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.80 % Allowed : 16.29 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.27), residues: 1060 helix: 1.11 (0.29), residues: 366 sheet: 0.07 (0.37), residues: 207 loop : -1.36 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.015 0.001 TYR R 204 PHE 0.030 0.001 PHE R 219 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8745) covalent geometry : angle 0.59430 (11834) SS BOND : bond 0.00114 ( 6) SS BOND : angle 1.53424 ( 12) hydrogen bonds : bond 0.03480 ( 376) hydrogen bonds : angle 4.24713 ( 1054) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8332 (mm-30) REVERT: A 213 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8709 (tp40) REVERT: A 220 HIS cc_start: 0.7946 (m-70) cc_final: 0.7683 (m-70) REVERT: B 16 ASN cc_start: 0.8896 (t0) cc_final: 0.8530 (m-40) REVERT: B 61 MET cc_start: 0.8972 (ppp) cc_final: 0.8453 (ppp) REVERT: B 260 GLU cc_start: 0.8716 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 262 MET cc_start: 0.8201 (tpp) cc_final: 0.7229 (tpp) REVERT: B 292 PHE cc_start: 0.8734 (m-80) cc_final: 0.8351 (m-80) REVERT: C 41 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 51 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7129 (mtm180) REVERT: N 112 GLU cc_start: 0.8566 (pm20) cc_final: 0.8338 (pm20) REVERT: R 184 ASP cc_start: 0.6907 (t0) cc_final: 0.6613 (t70) REVERT: R 219 PHE cc_start: 0.6400 (m-80) cc_final: 0.6196 (m-80) REVERT: R 221 PHE cc_start: 0.6865 (m-80) cc_final: 0.6364 (m-80) REVERT: R 298 MET cc_start: 0.7837 (mmp) cc_final: 0.7264 (mmm) outliers start: 26 outliers final: 21 residues processed: 193 average time/residue: 0.0950 time to fit residues: 24.5867 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.0070 chunk 88 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 110 ASN N 58 ASN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.160072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119668 restraints weight = 13652.374| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.58 r_work: 0.3438 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8751 Z= 0.121 Angle : 0.584 7.809 11846 Z= 0.295 Chirality : 0.042 0.147 1317 Planarity : 0.004 0.048 1505 Dihedral : 4.343 29.237 1183 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.24 % Allowed : 16.94 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.27), residues: 1060 helix: 1.21 (0.29), residues: 366 sheet: 0.03 (0.36), residues: 212 loop : -1.31 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.014 0.001 TYR R 204 PHE 0.025 0.001 PHE R 219 TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8745) covalent geometry : angle 0.58218 (11834) SS BOND : bond 0.00227 ( 6) SS BOND : angle 1.43810 ( 12) hydrogen bonds : bond 0.03376 ( 376) hydrogen bonds : angle 4.16203 ( 1054) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8315 (mm-30) REVERT: A 220 HIS cc_start: 0.7946 (m-70) cc_final: 0.7698 (m-70) REVERT: B 61 MET cc_start: 0.8924 (ppp) cc_final: 0.8452 (ppp) REVERT: B 111 TYR cc_start: 0.9142 (m-80) cc_final: 0.8867 (m-10) REVERT: B 260 GLU cc_start: 0.8680 (tt0) cc_final: 0.8210 (tm-30) REVERT: B 262 MET cc_start: 0.8248 (tpp) cc_final: 0.7273 (tpp) REVERT: B 292 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8273 (m-10) REVERT: C 41 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8323 (tm-30) REVERT: R 184 ASP cc_start: 0.6946 (t0) cc_final: 0.6568 (t70) REVERT: R 221 PHE cc_start: 0.6848 (m-80) cc_final: 0.6535 (m-80) REVERT: R 246 MET cc_start: 0.7876 (mmm) cc_final: 0.7675 (mmt) REVERT: R 298 MET cc_start: 0.7892 (mmp) cc_final: 0.7452 (mmm) outliers start: 30 outliers final: 26 residues processed: 189 average time/residue: 0.0991 time to fit residues: 25.7840 Evaluate side-chains 200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 102 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN N 58 ASN R 279 GLN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118499 restraints weight = 13560.734| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.67 r_work: 0.3466 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8751 Z= 0.110 Angle : 0.578 8.065 11846 Z= 0.291 Chirality : 0.041 0.153 1317 Planarity : 0.004 0.047 1505 Dihedral : 4.236 28.485 1183 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.80 % Allowed : 18.12 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.27), residues: 1060 helix: 1.27 (0.29), residues: 366 sheet: 0.22 (0.37), residues: 206 loop : -1.32 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.021 0.001 TYR R 441 PHE 0.018 0.001 PHE A 212 TRP 0.010 0.001 TRP A 234 HIS 0.002 0.000 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8745) covalent geometry : angle 0.57651 (11834) SS BOND : bond 0.00088 ( 6) SS BOND : angle 1.31132 ( 12) hydrogen bonds : bond 0.03196 ( 376) hydrogen bonds : angle 4.04230 ( 1054) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7849 (tt0) REVERT: A 220 HIS cc_start: 0.7952 (m-70) cc_final: 0.7732 (m-70) REVERT: B 61 MET cc_start: 0.8887 (ppp) cc_final: 0.8404 (ppp) REVERT: B 111 TYR cc_start: 0.9117 (m-80) cc_final: 0.8747 (m-10) REVERT: B 215 GLU cc_start: 0.8570 (pm20) cc_final: 0.8347 (pm20) REVERT: B 260 GLU cc_start: 0.8654 (tt0) cc_final: 0.8253 (tm-30) REVERT: B 262 MET cc_start: 0.8252 (tpp) cc_final: 0.7274 (tpp) REVERT: B 292 PHE cc_start: 0.8526 (m-80) cc_final: 0.8108 (m-80) REVERT: C 41 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 51 ARG cc_start: 0.7290 (mtp180) cc_final: 0.6983 (mtm180) REVERT: N 109 LEU cc_start: 0.8400 (tt) cc_final: 0.7998 (mp) REVERT: R 184 ASP cc_start: 0.6927 (t0) cc_final: 0.6546 (t70) REVERT: R 221 PHE cc_start: 0.6941 (m-80) cc_final: 0.6734 (m-80) REVERT: R 298 MET cc_start: 0.7838 (mmp) cc_final: 0.7413 (mmm) REVERT: R 416 LYS cc_start: 0.7737 (tppt) cc_final: 0.7051 (tmmt) outliers start: 26 outliers final: 21 residues processed: 193 average time/residue: 0.0985 time to fit residues: 26.1406 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 58 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.157104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115781 restraints weight = 13666.918| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.56 r_work: 0.3448 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8751 Z= 0.126 Angle : 0.603 8.266 11846 Z= 0.302 Chirality : 0.042 0.161 1317 Planarity : 0.004 0.047 1505 Dihedral : 4.221 28.620 1183 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.56 % Allowed : 17.91 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.27), residues: 1060 helix: 1.32 (0.29), residues: 365 sheet: 0.16 (0.37), residues: 211 loop : -1.29 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.020 0.001 TYR R 441 PHE 0.015 0.001 PHE B 292 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8745) covalent geometry : angle 0.60183 (11834) SS BOND : bond 0.00102 ( 6) SS BOND : angle 1.32100 ( 12) hydrogen bonds : bond 0.03248 ( 376) hydrogen bonds : angle 4.01914 ( 1054) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.9084 (m-80) cc_final: 0.8847 (m-10) REVERT: B 215 GLU cc_start: 0.8566 (pm20) cc_final: 0.8321 (pm20) REVERT: B 262 MET cc_start: 0.8209 (tpp) cc_final: 0.7549 (tpp) REVERT: B 292 PHE cc_start: 0.8651 (m-80) cc_final: 0.8235 (m-80) REVERT: C 41 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 53 LYS cc_start: 0.8545 (tptt) cc_final: 0.8302 (tptt) REVERT: N 109 LEU cc_start: 0.8448 (tt) cc_final: 0.8071 (mp) REVERT: R 184 ASP cc_start: 0.6915 (t0) cc_final: 0.6535 (t70) REVERT: R 221 PHE cc_start: 0.6968 (m-80) cc_final: 0.6750 (m-80) REVERT: R 416 LYS cc_start: 0.7720 (tppt) cc_final: 0.7441 (tppt) outliers start: 33 outliers final: 26 residues processed: 192 average time/residue: 0.1080 time to fit residues: 28.1597 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 71 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 58 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.158452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117047 restraints weight = 13533.269| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.56 r_work: 0.3469 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8751 Z= 0.114 Angle : 0.601 8.566 11846 Z= 0.300 Chirality : 0.042 0.153 1317 Planarity : 0.004 0.047 1505 Dihedral : 4.188 28.163 1183 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.91 % Allowed : 18.88 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.27), residues: 1060 helix: 1.36 (0.29), residues: 366 sheet: 0.18 (0.37), residues: 206 loop : -1.29 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.018 0.001 TYR R 441 PHE 0.016 0.001 PHE A 212 TRP 0.010 0.001 TRP A 234 HIS 0.002 0.000 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8745) covalent geometry : angle 0.60035 (11834) SS BOND : bond 0.00076 ( 6) SS BOND : angle 1.22219 ( 12) hydrogen bonds : bond 0.03145 ( 376) hydrogen bonds : angle 3.98007 ( 1054) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 251 SER cc_start: 0.8871 (p) cc_final: 0.8596 (m) REVERT: B 111 TYR cc_start: 0.9040 (m-80) cc_final: 0.8681 (m-10) REVERT: B 260 GLU cc_start: 0.8663 (tt0) cc_final: 0.8221 (tm-30) REVERT: B 280 LYS cc_start: 0.8539 (tttm) cc_final: 0.8252 (ttmm) REVERT: B 292 PHE cc_start: 0.8535 (m-80) cc_final: 0.8104 (m-80) REVERT: C 41 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 53 LYS cc_start: 0.8518 (tptt) cc_final: 0.8265 (tptt) REVERT: N 109 LEU cc_start: 0.8472 (tt) cc_final: 0.8150 (mp) REVERT: R 184 ASP cc_start: 0.6917 (t0) cc_final: 0.6545 (t70) REVERT: R 221 PHE cc_start: 0.6933 (m-80) cc_final: 0.6311 (m-80) REVERT: R 298 MET cc_start: 0.7793 (mmp) cc_final: 0.7121 (mmm) REVERT: R 367 ASP cc_start: 0.8182 (m-30) cc_final: 0.7972 (m-30) REVERT: R 416 LYS cc_start: 0.7684 (tppt) cc_final: 0.7398 (tppt) outliers start: 27 outliers final: 24 residues processed: 188 average time/residue: 0.0982 time to fit residues: 25.6397 Evaluate side-chains 198 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 58 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117128 restraints weight = 13480.570| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.55 r_work: 0.3467 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8751 Z= 0.117 Angle : 0.616 9.199 11846 Z= 0.307 Chirality : 0.042 0.153 1317 Planarity : 0.004 0.044 1505 Dihedral : 4.139 28.083 1183 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 18.45 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.27), residues: 1060 helix: 1.37 (0.29), residues: 366 sheet: 0.20 (0.37), residues: 206 loop : -1.28 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.017 0.001 TYR R 441 PHE 0.028 0.001 PHE R 496 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.000 HIS R 181 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8745) covalent geometry : angle 0.61484 (11834) SS BOND : bond 0.00090 ( 6) SS BOND : angle 1.20863 ( 12) hydrogen bonds : bond 0.03139 ( 376) hydrogen bonds : angle 3.97785 ( 1054) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 SER cc_start: 0.8876 (p) cc_final: 0.8601 (m) REVERT: B 111 TYR cc_start: 0.9013 (m-80) cc_final: 0.8680 (m-10) REVERT: B 260 GLU cc_start: 0.8665 (tt0) cc_final: 0.8227 (tm-30) REVERT: B 280 LYS cc_start: 0.8519 (tttm) cc_final: 0.8239 (ttmm) REVERT: B 292 PHE cc_start: 0.8563 (m-80) cc_final: 0.8147 (m-80) REVERT: C 41 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 53 LYS cc_start: 0.8501 (tptt) cc_final: 0.8231 (tptt) REVERT: N 109 LEU cc_start: 0.8447 (tt) cc_final: 0.8084 (mp) REVERT: R 184 ASP cc_start: 0.6925 (t0) cc_final: 0.6549 (t70) REVERT: R 221 PHE cc_start: 0.6741 (m-80) cc_final: 0.6381 (m-80) REVERT: R 246 MET cc_start: 0.8203 (mmm) cc_final: 0.7730 (mmp) REVERT: R 298 MET cc_start: 0.7846 (mmp) cc_final: 0.7140 (mmm) REVERT: R 416 LYS cc_start: 0.7712 (tppt) cc_final: 0.7484 (tppt) outliers start: 30 outliers final: 23 residues processed: 185 average time/residue: 0.0922 time to fit residues: 23.3736 Evaluate side-chains 191 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS N 58 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.155430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113739 restraints weight = 13580.737| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.55 r_work: 0.3418 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8751 Z= 0.158 Angle : 0.645 8.719 11846 Z= 0.323 Chirality : 0.043 0.184 1317 Planarity : 0.004 0.043 1505 Dihedral : 4.221 29.150 1183 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.91 % Allowed : 18.88 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.27), residues: 1060 helix: 1.27 (0.28), residues: 374 sheet: 0.06 (0.36), residues: 217 loop : -1.24 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 90 TYR 0.019 0.002 TYR R 245 PHE 0.027 0.002 PHE R 496 TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8745) covalent geometry : angle 0.64399 (11834) SS BOND : bond 0.00090 ( 6) SS BOND : angle 1.37315 ( 12) hydrogen bonds : bond 0.03332 ( 376) hydrogen bonds : angle 4.04638 ( 1054) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8053 (mmp80) cc_final: 0.7289 (mpt180) REVERT: A 251 SER cc_start: 0.8898 (p) cc_final: 0.8422 (m) REVERT: B 105 TYR cc_start: 0.9357 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 260 GLU cc_start: 0.8718 (tt0) cc_final: 0.8279 (tm-30) REVERT: B 262 MET cc_start: 0.8204 (tpp) cc_final: 0.7290 (tpp) REVERT: C 41 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 51 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6890 (mtm180) REVERT: C 53 LYS cc_start: 0.8576 (tptt) cc_final: 0.8252 (tptt) REVERT: N 109 LEU cc_start: 0.8465 (tt) cc_final: 0.8090 (mp) REVERT: R 184 ASP cc_start: 0.6996 (t0) cc_final: 0.6604 (t70) REVERT: R 221 PHE cc_start: 0.6836 (m-80) cc_final: 0.6181 (m-80) REVERT: R 246 MET cc_start: 0.8252 (mmm) cc_final: 0.7360 (mmm) REVERT: R 298 MET cc_start: 0.7932 (mmp) cc_final: 0.7448 (mmm) outliers start: 27 outliers final: 23 residues processed: 186 average time/residue: 0.0866 time to fit residues: 22.1783 Evaluate side-chains 192 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 283 ASN Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS N 58 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115934 restraints weight = 13496.715| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.53 r_work: 0.3449 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8751 Z= 0.130 Angle : 0.652 8.814 11846 Z= 0.325 Chirality : 0.042 0.174 1317 Planarity : 0.004 0.043 1505 Dihedral : 4.235 28.565 1183 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.80 % Allowed : 19.96 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.27), residues: 1060 helix: 1.24 (0.28), residues: 374 sheet: 0.08 (0.36), residues: 211 loop : -1.21 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 90 TYR 0.017 0.001 TYR R 245 PHE 0.026 0.001 PHE R 496 TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8745) covalent geometry : angle 0.64905 (11834) SS BOND : bond 0.00158 ( 6) SS BOND : angle 2.05843 ( 12) hydrogen bonds : bond 0.03233 ( 376) hydrogen bonds : angle 4.00747 ( 1054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.08 seconds wall clock time: 42 minutes 37.43 seconds (2557.43 seconds total)