Starting phenix.real_space_refine on Fri Aug 22 22:29:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvm_32144/08_2025/7vvm_32144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvm_32144/08_2025/7vvm_32144.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/7vvm_32144/08_2025/7vvm_32144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvm_32144/08_2025/7vvm_32144.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvm_32144/08_2025/7vvm_32144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvm_32144/08_2025/7vvm_32144.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= 0.001 sd= 0.008 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 52 5.16 5 C 5405 2.51 5 N 1486 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 8507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1893 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2508 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 389 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 217 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2536 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 3, 'PHE:plan': 3, 'HIS:plan': 5, 'ARG:plan': 11, 'TRP:plan': 5, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 2.35, per 1000 atoms: 0.28 Number of scatterers: 8507 At special positions: 0 Unit cell: (127.267, 105.134, 126.16, 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 52 16.00 O 1564 8.00 N 1486 7.00 C 5405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 459.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 41.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.269A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.503A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.503A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.518A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.945A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.562A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.677A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.575A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.687A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL R 193 " --> pdb=" O MET R 189 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.570A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.923A pdb=" N VAL R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 347 removed outlier: 3.763A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.619A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 391 removed outlier: 3.570A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.617A pdb=" N LEU R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 418 removed outlier: 3.700A pdb=" N TYR R 403 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.633A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.511A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.691A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.750A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.823A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.711A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.501A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.426A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.604A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.576A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 449 hydrogen bonds defined for protein. 1257 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: 1.43 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1409 1.31 - 1.44: 2401 1.44 - 1.58: 4798 1.58 - 1.72: 0 1.72 - 1.85: 76 Bond restraints: 8684 Sorted by residual: bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.503 -0.043 7.50e-03 1.78e+04 3.30e+01 bond pdb=" C ALA B 287 " pdb=" O ALA B 287 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.21e-02 6.83e+03 2.97e+01 bond pdb=" C VAL B 100 " pdb=" O VAL B 100 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.04e-02 9.25e+03 2.96e+01 bond pdb=" C TYR B 124 " pdb=" O TYR B 124 " ideal model delta sigma weight residual 1.236 1.301 -0.065 1.21e-02 6.83e+03 2.88e+01 bond pdb=" CE1 HIS A 377 " pdb=" NE2 HIS A 377 " ideal model delta sigma weight residual 1.321 1.371 -0.050 1.00e-02 1.00e+04 2.46e+01 ... (remaining 8679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 9024 2.13 - 4.26: 2633 4.26 - 6.39: 142 6.39 - 8.52: 6 8.52 - 10.65: 2 Bond angle restraints: 11807 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 113.57 120.74 -7.17 1.31e+00 5.83e-01 2.99e+01 angle pdb=" N GLN R 451 " pdb=" CA GLN R 451 " pdb=" C GLN R 451 " ideal model delta sigma weight residual 110.97 105.73 5.24 1.09e+00 8.42e-01 2.32e+01 angle pdb=" CA VAL R 439 " pdb=" C VAL R 439 " pdb=" O VAL R 439 " ideal model delta sigma weight residual 121.05 115.76 5.29 1.11e+00 8.12e-01 2.27e+01 angle pdb=" N ILE A 372 " pdb=" CA ILE A 372 " pdb=" C ILE A 372 " ideal model delta sigma weight residual 110.72 106.02 4.70 1.01e+00 9.80e-01 2.16e+01 angle pdb=" C LYS R 34 " pdb=" N GLU R 35 " pdb=" CA GLU R 35 " ideal model delta sigma weight residual 120.54 126.82 -6.28 1.35e+00 5.49e-01 2.16e+01 ... (remaining 11802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 4632 16.64 - 33.28: 396 33.28 - 49.92: 56 49.92 - 66.56: 13 66.56 - 83.20: 14 Dihedral angle restraints: 5111 sinusoidal: 1822 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 649 0.058 - 0.117: 466 0.117 - 0.175: 186 0.175 - 0.233: 44 0.233 - 0.291: 7 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA PRO A 351 " pdb=" N PRO A 351 " pdb=" C PRO A 351 " pdb=" CB PRO A 351 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1349 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.013 2.00e-02 2.50e+03 1.04e-02 2.68e+00 pdb=" CG TRP A 234 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 378 " -0.020 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE R 378 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 378 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 378 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 378 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 378 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 352 " 0.015 2.00e-02 2.50e+03 1.20e-02 2.14e+00 pdb=" CG HIS A 352 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS A 352 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 352 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 352 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 352 " 0.007 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 8636 3.28 - 3.82: 13249 3.82 - 4.36: 17850 4.36 - 4.90: 29450 Nonbonded interactions: 69701 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.200 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.300 3.040 nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.304 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.322 3.040 ... (remaining 69696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.015 0.101 8687 Z= 1.075 Angle : 1.763 10.650 11813 Z= 1.280 Chirality : 0.086 0.291 1352 Planarity : 0.003 0.012 1514 Dihedral : 13.507 83.200 2972 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.60 % Allowed : 4.06 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.24), residues: 1113 helix: -0.46 (0.23), residues: 430 sheet: -0.85 (0.33), residues: 226 loop : -0.84 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.015 0.003 TYR N 60 PHE 0.020 0.003 PHE R 378 TRP 0.018 0.004 TRP B 297 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.01492 ( 8684) covalent geometry : angle 1.76130 (11807) SS BOND : bond 0.02298 ( 3) SS BOND : angle 3.57293 ( 6) hydrogen bonds : bond 0.25295 ( 437) hydrogen bonds : angle 8.76817 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.238 Fit side-chains REVERT: A 16 GLU cc_start: 0.6489 (tp30) cc_final: 0.5699 (tm-30) REVERT: A 216 LYS cc_start: 0.7371 (mptt) cc_final: 0.7127 (mmtt) REVERT: A 221 MET cc_start: 0.7791 (ttt) cc_final: 0.7457 (ttp) REVERT: A 258 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7217 (mp0) REVERT: A 325 THR cc_start: 0.8530 (m) cc_final: 0.8325 (m) REVERT: A 379 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6980 (ttm110) REVERT: A 382 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 80 ILE cc_start: 0.8221 (mt) cc_final: 0.8021 (mm) REVERT: B 137 ARG cc_start: 0.6551 (ttm110) cc_final: 0.5769 (ttm-80) REVERT: B 181 THR cc_start: 0.7741 (m) cc_final: 0.7530 (p) REVERT: B 197 ARG cc_start: 0.6105 (mmp-170) cc_final: 0.5892 (mmm160) REVERT: B 220 GLN cc_start: 0.7424 (mt0) cc_final: 0.6993 (mt0) REVERT: B 264 TYR cc_start: 0.7883 (m-80) cc_final: 0.7269 (m-80) REVERT: B 277 SER cc_start: 0.8783 (t) cc_final: 0.8316 (m) REVERT: B 289 TYR cc_start: 0.9113 (m-80) cc_final: 0.8723 (m-80) REVERT: B 322 ASP cc_start: 0.7872 (m-30) cc_final: 0.7023 (t0) REVERT: G 42 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6939 (mt-10) REVERT: G 44 HIS cc_start: 0.6819 (m90) cc_final: 0.6608 (m170) REVERT: G 62 ARG cc_start: 0.4738 (pmt-80) cc_final: 0.3603 (mmm160) REVERT: N 3 GLN cc_start: 0.6269 (tt0) cc_final: 0.5545 (tp-100) REVERT: N 19 ARG cc_start: 0.7322 (ttt90) cc_final: 0.7062 (ttt-90) REVERT: N 82 GLN cc_start: 0.6016 (tp40) cc_final: 0.5136 (tp-100) REVERT: N 83 MET cc_start: 0.6351 (mtt) cc_final: 0.5925 (mpp) REVERT: N 93 VAL cc_start: 0.7778 (t) cc_final: 0.7540 (p) REVERT: N 94 TYR cc_start: 0.8466 (m-80) cc_final: 0.7815 (m-80) REVERT: R 282 ARG cc_start: 0.7013 (mpt-90) cc_final: 0.6724 (mmt90) REVERT: R 291 PHE cc_start: 0.8031 (m-10) cc_final: 0.7733 (m-10) REVERT: R 360 LYS cc_start: 0.4708 (ptmt) cc_final: 0.4498 (ptmt) REVERT: R 363 ILE cc_start: 0.7763 (mm) cc_final: 0.7487 (tt) REVERT: R 372 VAL cc_start: 0.7205 (m) cc_final: 0.6989 (t) REVERT: R 383 ARG cc_start: 0.6956 (tmm-80) cc_final: 0.6714 (tmm-80) REVERT: R 391 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7566 (mt-10) REVERT: R 399 THR cc_start: 0.5947 (t) cc_final: 0.5636 (p) REVERT: R 439 VAL cc_start: 0.4753 (p) cc_final: 0.4292 (m) REVERT: R 443 TYR cc_start: 0.7097 (t80) cc_final: 0.6775 (t80) REVERT: R 445 MET cc_start: 0.7668 (mmm) cc_final: 0.7223 (mmp) REVERT: R 462 CYS cc_start: 0.6426 (m) cc_final: 0.6098 (t) REVERT: R 473 SER cc_start: 0.4742 (m) cc_final: 0.4528 (t) outliers start: 5 outliers final: 2 residues processed: 206 average time/residue: 0.1241 time to fit residues: 32.6101 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 254 ASN A 284 GLN B 239 ASN B 340 ASN N 39 GLN P 14 HIS R 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134866 restraints weight = 10941.753| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.17 r_work: 0.3437 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8687 Z= 0.135 Angle : 0.546 6.025 11813 Z= 0.300 Chirality : 0.041 0.152 1352 Planarity : 0.003 0.028 1514 Dihedral : 4.489 33.563 1217 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.27 % Allowed : 9.67 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1113 helix: 1.06 (0.25), residues: 433 sheet: -0.50 (0.34), residues: 219 loop : -0.47 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 72 TYR 0.020 0.001 TYR R 191 PHE 0.015 0.001 PHE R 335 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8684) covalent geometry : angle 0.54600 (11807) SS BOND : bond 0.00112 ( 3) SS BOND : angle 1.06657 ( 6) hydrogen bonds : bond 0.05299 ( 437) hydrogen bonds : angle 5.41078 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6869 (tppt) cc_final: 0.6225 (tmtt) REVERT: A 216 LYS cc_start: 0.7115 (mptt) cc_final: 0.6705 (mmtt) REVERT: A 258 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7336 (mp0) REVERT: A 379 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6526 (ttp-110) REVERT: B 20 ASP cc_start: 0.6934 (m-30) cc_final: 0.6606 (m-30) REVERT: B 68 ARG cc_start: 0.7395 (ttt180) cc_final: 0.7110 (ttt90) REVERT: B 82 TRP cc_start: 0.8519 (m100) cc_final: 0.8152 (m100) REVERT: B 137 ARG cc_start: 0.6476 (ttm110) cc_final: 0.5897 (ttm-80) REVERT: B 188 MET cc_start: 0.7836 (mmm) cc_final: 0.7505 (mmp) REVERT: B 197 ARG cc_start: 0.6205 (mmp-170) cc_final: 0.5976 (mmm160) REVERT: B 220 GLN cc_start: 0.7334 (mt0) cc_final: 0.7093 (tt0) REVERT: B 262 MET cc_start: 0.7079 (tpp) cc_final: 0.6840 (tpt) REVERT: B 264 TYR cc_start: 0.7545 (m-80) cc_final: 0.7083 (m-80) REVERT: B 277 SER cc_start: 0.8663 (t) cc_final: 0.8226 (m) REVERT: B 322 ASP cc_start: 0.7440 (m-30) cc_final: 0.6698 (t0) REVERT: G 42 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6974 (mt-10) REVERT: G 44 HIS cc_start: 0.6989 (m90) cc_final: 0.6704 (m-70) REVERT: G 62 ARG cc_start: 0.4755 (pmt-80) cc_final: 0.3599 (mmm-85) REVERT: N 77 ASN cc_start: 0.6827 (m-40) cc_final: 0.6509 (t0) REVERT: N 82 GLN cc_start: 0.6521 (tp40) cc_final: 0.6132 (tp-100) REVERT: N 93 VAL cc_start: 0.7705 (t) cc_final: 0.7366 (p) REVERT: N 94 TYR cc_start: 0.8160 (m-80) cc_final: 0.7691 (m-80) REVERT: R 186 ARG cc_start: 0.4258 (mtt180) cc_final: 0.3888 (mtt180) REVERT: R 315 PHE cc_start: 0.5729 (t80) cc_final: 0.5523 (t80) REVERT: R 331 LEU cc_start: 0.7292 (tt) cc_final: 0.7081 (tp) REVERT: R 360 LYS cc_start: 0.5076 (ptmt) cc_final: 0.4817 (ptmt) REVERT: R 391 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6788 (mt-10) REVERT: R 399 THR cc_start: 0.5993 (t) cc_final: 0.5634 (m) REVERT: R 439 VAL cc_start: 0.4928 (p) cc_final: 0.4417 (m) REVERT: R 441 MET cc_start: 0.5832 (mmt) cc_final: 0.5291 (mmt) REVERT: R 445 MET cc_start: 0.7244 (mmm) cc_final: 0.6996 (mmt) REVERT: R 465 GLU cc_start: 0.6122 (tp30) cc_final: 0.5904 (tp30) outliers start: 19 outliers final: 11 residues processed: 177 average time/residue: 0.1041 time to fit residues: 24.4044 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 78 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 75 GLN B 155 ASN P 9 HIS R 295 ASN R 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133470 restraints weight = 10869.004| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.14 r_work: 0.3420 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8687 Z= 0.143 Angle : 0.520 5.569 11813 Z= 0.284 Chirality : 0.042 0.160 1352 Planarity : 0.004 0.033 1514 Dihedral : 4.158 18.025 1215 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.51 % Allowed : 12.41 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.26), residues: 1113 helix: 1.29 (0.26), residues: 433 sheet: -0.26 (0.35), residues: 214 loop : -0.44 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.018 0.002 TYR R 191 PHE 0.017 0.002 PHE R 335 TRP 0.018 0.002 TRP B 82 HIS 0.008 0.002 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8684) covalent geometry : angle 0.51971 (11807) SS BOND : bond 0.00137 ( 3) SS BOND : angle 0.64776 ( 6) hydrogen bonds : bond 0.04427 ( 437) hydrogen bonds : angle 4.88206 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7057 (tppt) cc_final: 0.6454 (tmtt) REVERT: A 51 SER cc_start: 0.8341 (m) cc_final: 0.7951 (p) REVERT: A 59 GLN cc_start: 0.6397 (mt0) cc_final: 0.6063 (mm-40) REVERT: A 216 LYS cc_start: 0.7173 (mptt) cc_final: 0.6708 (mmtt) REVERT: A 240 ASP cc_start: 0.7258 (p0) cc_final: 0.7049 (p0) REVERT: A 258 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7304 (mp0) REVERT: B 20 ASP cc_start: 0.6651 (m-30) cc_final: 0.6293 (m-30) REVERT: B 68 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7150 (ttt90) REVERT: B 137 ARG cc_start: 0.6660 (ttm110) cc_final: 0.5929 (ttm-80) REVERT: B 197 ARG cc_start: 0.6276 (mmp-170) cc_final: 0.5667 (mmm160) REVERT: B 220 GLN cc_start: 0.7322 (mt0) cc_final: 0.7026 (mt0) REVERT: B 262 MET cc_start: 0.6715 (tpp) cc_final: 0.6469 (tpt) REVERT: B 263 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7581 (m) REVERT: B 264 TYR cc_start: 0.7569 (m-80) cc_final: 0.7084 (m-80) REVERT: B 277 SER cc_start: 0.8662 (t) cc_final: 0.8237 (m) REVERT: B 322 ASP cc_start: 0.7516 (m-30) cc_final: 0.6689 (t0) REVERT: G 42 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6957 (mt-10) REVERT: G 44 HIS cc_start: 0.6856 (m90) cc_final: 0.6481 (m-70) REVERT: G 62 ARG cc_start: 0.4729 (pmt-80) cc_final: 0.3692 (mmm160) REVERT: N 77 ASN cc_start: 0.6573 (m-40) cc_final: 0.6249 (t0) REVERT: N 94 TYR cc_start: 0.8244 (m-80) cc_final: 0.7655 (m-80) REVERT: N 106 ASP cc_start: 0.6978 (p0) cc_final: 0.6421 (p0) REVERT: R 240 LYS cc_start: 0.5887 (mmmm) cc_final: 0.5354 (tptp) REVERT: R 405 LYS cc_start: 0.6516 (ttmm) cc_final: 0.6236 (tppt) REVERT: R 407 LEU cc_start: 0.7219 (tp) cc_final: 0.7011 (mt) REVERT: R 439 VAL cc_start: 0.5070 (p) cc_final: 0.4557 (m) REVERT: R 441 MET cc_start: 0.5836 (mmt) cc_final: 0.5407 (mmt) REVERT: R 465 GLU cc_start: 0.5702 (tp30) cc_final: 0.5477 (tp30) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 0.0952 time to fit residues: 20.4836 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 254 ASN R 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134425 restraints weight = 11128.055| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.19 r_work: 0.3430 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8687 Z= 0.125 Angle : 0.486 5.622 11813 Z= 0.266 Chirality : 0.041 0.161 1352 Planarity : 0.003 0.038 1514 Dihedral : 4.027 16.496 1215 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 13.37 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.26), residues: 1113 helix: 1.40 (0.25), residues: 434 sheet: -0.14 (0.34), residues: 214 loop : -0.39 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.019 0.001 TYR R 191 PHE 0.019 0.001 PHE R 335 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8684) covalent geometry : angle 0.48605 (11807) SS BOND : bond 0.00026 ( 3) SS BOND : angle 0.43081 ( 6) hydrogen bonds : bond 0.04010 ( 437) hydrogen bonds : angle 4.66872 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6345 (mt0) cc_final: 0.6055 (mm-40) REVERT: A 216 LYS cc_start: 0.7055 (mptt) cc_final: 0.6559 (mmtt) REVERT: A 240 ASP cc_start: 0.7565 (p0) cc_final: 0.7356 (p0) REVERT: A 258 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7415 (mp0) REVERT: A 337 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6235 (ttp-110) REVERT: A 379 ARG cc_start: 0.6885 (ttm110) cc_final: 0.6676 (ttm110) REVERT: B 20 ASP cc_start: 0.6496 (m-30) cc_final: 0.6156 (m-30) REVERT: B 68 ARG cc_start: 0.7426 (ttt180) cc_final: 0.6988 (ttt90) REVERT: B 137 ARG cc_start: 0.6642 (ttm110) cc_final: 0.5928 (ttm-80) REVERT: B 220 GLN cc_start: 0.7385 (mt0) cc_final: 0.7169 (tt0) REVERT: B 263 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7395 (m) REVERT: B 277 SER cc_start: 0.8659 (t) cc_final: 0.8218 (m) REVERT: B 322 ASP cc_start: 0.7503 (m-30) cc_final: 0.6680 (t0) REVERT: G 42 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6977 (mt-10) REVERT: G 62 ARG cc_start: 0.4965 (pmt-80) cc_final: 0.3775 (mmm160) REVERT: N 46 GLU cc_start: 0.7553 (pt0) cc_final: 0.7115 (mt-10) REVERT: N 77 ASN cc_start: 0.6495 (m-40) cc_final: 0.6153 (t0) REVERT: N 94 TYR cc_start: 0.8225 (m-80) cc_final: 0.7655 (m-80) REVERT: N 106 ASP cc_start: 0.7096 (p0) cc_final: 0.6513 (p0) REVERT: R 233 ARG cc_start: 0.7352 (ttt180) cc_final: 0.7124 (ttt180) REVERT: R 240 LYS cc_start: 0.5833 (mmmm) cc_final: 0.5453 (tptp) REVERT: R 441 MET cc_start: 0.5889 (mmt) cc_final: 0.5437 (mmt) REVERT: R 465 GLU cc_start: 0.5821 (tp30) cc_final: 0.5560 (tp30) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.1113 time to fit residues: 23.6541 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 GLN R 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134552 restraints weight = 11031.225| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.15 r_work: 0.3453 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8687 Z= 0.131 Angle : 0.480 5.580 11813 Z= 0.263 Chirality : 0.041 0.165 1352 Planarity : 0.003 0.038 1514 Dihedral : 4.013 15.904 1215 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.22 % Allowed : 14.68 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.53 (0.26), residues: 1113 helix: 1.43 (0.25), residues: 435 sheet: -0.11 (0.34), residues: 214 loop : -0.35 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 181 TYR 0.018 0.001 TYR R 191 PHE 0.022 0.002 PHE R 315 TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8684) covalent geometry : angle 0.48042 (11807) SS BOND : bond 0.00034 ( 3) SS BOND : angle 0.50144 ( 6) hydrogen bonds : bond 0.03925 ( 437) hydrogen bonds : angle 4.56624 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 51 SER cc_start: 0.8357 (m) cc_final: 0.7952 (p) REVERT: A 59 GLN cc_start: 0.6227 (mt0) cc_final: 0.5976 (mm-40) REVERT: A 216 LYS cc_start: 0.7118 (mptt) cc_final: 0.6626 (mmtt) REVERT: A 240 ASP cc_start: 0.7507 (p0) cc_final: 0.7297 (p0) REVERT: A 258 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 346 ARG cc_start: 0.6313 (mtt180) cc_final: 0.6017 (mmt-90) REVERT: B 68 ARG cc_start: 0.7395 (ttt180) cc_final: 0.7016 (ttt90) REVERT: B 137 ARG cc_start: 0.6679 (ttm110) cc_final: 0.6035 (ttm-80) REVERT: B 220 GLN cc_start: 0.7450 (mt0) cc_final: 0.7107 (tt0) REVERT: B 263 THR cc_start: 0.7343 (OUTLIER) cc_final: 0.7054 (m) REVERT: B 264 TYR cc_start: 0.7491 (m-80) cc_final: 0.7052 (m-80) REVERT: B 277 SER cc_start: 0.8603 (t) cc_final: 0.8200 (m) REVERT: B 322 ASP cc_start: 0.7517 (m-30) cc_final: 0.6761 (t0) REVERT: G 42 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7109 (mt-10) REVERT: G 62 ARG cc_start: 0.5000 (pmt-80) cc_final: 0.3815 (mmm-85) REVERT: N 46 GLU cc_start: 0.7658 (pt0) cc_final: 0.7369 (mt-10) REVERT: N 77 ASN cc_start: 0.6426 (m-40) cc_final: 0.6163 (t0) REVERT: N 94 TYR cc_start: 0.8172 (m-80) cc_final: 0.7743 (m-80) REVERT: N 106 ASP cc_start: 0.7089 (p0) cc_final: 0.6550 (p0) REVERT: R 231 MET cc_start: 0.7391 (mtp) cc_final: 0.6966 (mtp) REVERT: R 233 ARG cc_start: 0.7409 (ttt180) cc_final: 0.7205 (ttt180) REVERT: R 292 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6807 (tp) REVERT: R 441 MET cc_start: 0.6072 (mmt) cc_final: 0.5675 (mmt) REVERT: R 465 GLU cc_start: 0.5942 (tp30) cc_final: 0.5673 (tp30) outliers start: 27 outliers final: 21 residues processed: 155 average time/residue: 0.1097 time to fit residues: 22.8423 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129521 restraints weight = 11290.713| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.05 r_work: 0.3462 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8687 Z= 0.221 Angle : 0.584 5.802 11813 Z= 0.318 Chirality : 0.044 0.171 1352 Planarity : 0.005 0.043 1514 Dihedral : 4.576 17.394 1215 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.70 % Allowed : 16.71 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.25), residues: 1113 helix: 0.89 (0.25), residues: 442 sheet: -0.36 (0.32), residues: 223 loop : -0.51 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 38 TYR 0.024 0.002 TYR R 191 PHE 0.022 0.002 PHE R 315 TRP 0.016 0.002 TRP R 298 HIS 0.007 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 8684) covalent geometry : angle 0.58414 (11807) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.89456 ( 6) hydrogen bonds : bond 0.04540 ( 437) hydrogen bonds : angle 4.91028 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7012 (mptt) cc_final: 0.6669 (mmtt) REVERT: A 240 ASP cc_start: 0.7533 (p0) cc_final: 0.7268 (p0) REVERT: A 254 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7506 (t0) REVERT: A 258 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7459 (mp0) REVERT: B 68 ARG cc_start: 0.7393 (ttt180) cc_final: 0.7091 (ttt90) REVERT: B 137 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6139 (ttm-80) REVERT: B 220 GLN cc_start: 0.7443 (mt0) cc_final: 0.6984 (tt0) REVERT: B 263 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.6991 (m) REVERT: B 277 SER cc_start: 0.8606 (t) cc_final: 0.8187 (m) REVERT: B 322 ASP cc_start: 0.7539 (m-30) cc_final: 0.6877 (t0) REVERT: G 42 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7025 (mt-10) REVERT: G 58 GLU cc_start: 0.6897 (pm20) cc_final: 0.6657 (pm20) REVERT: N 77 ASN cc_start: 0.6578 (m-40) cc_final: 0.6252 (t0) REVERT: N 94 TYR cc_start: 0.8206 (m-80) cc_final: 0.7917 (m-80) REVERT: N 124 VAL cc_start: 0.8186 (t) cc_final: 0.7980 (p) REVERT: R 240 LYS cc_start: 0.6277 (mmtp) cc_final: 0.5952 (tptp) REVERT: R 441 MET cc_start: 0.6099 (mmt) cc_final: 0.5447 (mmt) REVERT: R 465 GLU cc_start: 0.5926 (tp30) cc_final: 0.5702 (tp30) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.1031 time to fit residues: 20.8134 Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN P 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133833 restraints weight = 11294.148| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.10 r_work: 0.3512 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8687 Z= 0.104 Angle : 0.470 6.165 11813 Z= 0.257 Chirality : 0.040 0.158 1352 Planarity : 0.003 0.038 1514 Dihedral : 4.059 18.792 1215 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.10 % Allowed : 17.90 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1113 helix: 1.56 (0.26), residues: 432 sheet: -0.17 (0.33), residues: 219 loop : -0.38 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.014 0.001 TYR R 191 PHE 0.028 0.001 PHE R 315 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8684) covalent geometry : angle 0.47035 (11807) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.62029 ( 6) hydrogen bonds : bond 0.03664 ( 437) hydrogen bonds : angle 4.50049 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6409 (mt0) cc_final: 0.6129 (mm-40) REVERT: A 216 LYS cc_start: 0.6920 (mptt) cc_final: 0.6529 (mmtt) REVERT: A 240 ASP cc_start: 0.7348 (p0) cc_final: 0.7104 (p0) REVERT: A 258 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7319 (mp0) REVERT: B 68 ARG cc_start: 0.7448 (ttt180) cc_final: 0.7086 (ttt90) REVERT: B 220 GLN cc_start: 0.7335 (mt0) cc_final: 0.7105 (tt0) REVERT: B 262 MET cc_start: 0.6979 (tpt) cc_final: 0.6742 (tpt) REVERT: B 263 THR cc_start: 0.7260 (OUTLIER) cc_final: 0.7013 (m) REVERT: B 264 TYR cc_start: 0.7344 (m-80) cc_final: 0.6913 (m-80) REVERT: B 277 SER cc_start: 0.8552 (t) cc_final: 0.8166 (m) REVERT: B 322 ASP cc_start: 0.7474 (m-30) cc_final: 0.6772 (t0) REVERT: G 42 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7124 (mt-10) REVERT: G 58 GLU cc_start: 0.6816 (pm20) cc_final: 0.6599 (pm20) REVERT: N 94 TYR cc_start: 0.8057 (m-80) cc_final: 0.7642 (m-80) REVERT: R 231 MET cc_start: 0.7495 (mtp) cc_final: 0.7036 (mtp) REVERT: R 441 MET cc_start: 0.6020 (mmt) cc_final: 0.5652 (mmt) REVERT: R 465 GLU cc_start: 0.6026 (tp30) cc_final: 0.5745 (tp30) outliers start: 26 outliers final: 19 residues processed: 160 average time/residue: 0.1147 time to fit residues: 24.1900 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 254 ASN B 88 ASN R 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129089 restraints weight = 11526.392| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.98 r_work: 0.3455 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 8687 Z= 0.294 Angle : 0.668 6.649 11813 Z= 0.361 Chirality : 0.048 0.175 1352 Planarity : 0.005 0.060 1514 Dihedral : 4.895 18.851 1215 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.82 % Allowed : 17.54 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1113 helix: 0.56 (0.25), residues: 441 sheet: -0.60 (0.32), residues: 235 loop : -0.78 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 233 TYR 0.029 0.003 TYR R 191 PHE 0.019 0.003 PHE R 315 TRP 0.019 0.003 TRP R 298 HIS 0.010 0.002 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 8684) covalent geometry : angle 0.66784 (11807) SS BOND : bond 0.00309 ( 3) SS BOND : angle 1.43508 ( 6) hydrogen bonds : bond 0.04871 ( 437) hydrogen bonds : angle 5.12457 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7037 (mptt) cc_final: 0.6641 (mmtt) REVERT: A 240 ASP cc_start: 0.7536 (p0) cc_final: 0.7270 (p0) REVERT: A 254 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7569 (m-40) REVERT: A 258 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7513 (mp0) REVERT: B 137 ARG cc_start: 0.6543 (ttm-80) cc_final: 0.5649 (ttm-80) REVERT: B 181 THR cc_start: 0.8280 (m) cc_final: 0.7999 (m) REVERT: B 220 GLN cc_start: 0.7393 (mt0) cc_final: 0.6938 (tt0) REVERT: B 277 SER cc_start: 0.8590 (t) cc_final: 0.8137 (m) REVERT: B 322 ASP cc_start: 0.7571 (m-30) cc_final: 0.6936 (t0) REVERT: G 42 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6984 (tm-30) REVERT: N 46 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7101 (mt-10) REVERT: N 74 ASN cc_start: 0.7818 (m-40) cc_final: 0.7416 (m-40) REVERT: N 77 ASN cc_start: 0.6184 (t0) cc_final: 0.5971 (t0) REVERT: N 94 TYR cc_start: 0.8218 (m-80) cc_final: 0.7967 (m-80) REVERT: N 124 VAL cc_start: 0.8162 (t) cc_final: 0.7956 (p) REVERT: R 441 MET cc_start: 0.6128 (mmt) cc_final: 0.5514 (mmt) REVERT: R 465 GLU cc_start: 0.5914 (tp30) cc_final: 0.5700 (tp30) outliers start: 32 outliers final: 26 residues processed: 150 average time/residue: 0.0996 time to fit residues: 20.4503 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 88 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132140 restraints weight = 11365.292| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.11 r_work: 0.3502 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8687 Z= 0.121 Angle : 0.512 7.507 11813 Z= 0.276 Chirality : 0.041 0.189 1352 Planarity : 0.004 0.040 1514 Dihedral : 4.287 18.320 1215 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.98 % Allowed : 18.85 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.26), residues: 1113 helix: 1.19 (0.25), residues: 439 sheet: -0.47 (0.32), residues: 233 loop : -0.57 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.018 0.001 TYR R 191 PHE 0.030 0.002 PHE R 315 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS P 9 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8684) covalent geometry : angle 0.51173 (11807) SS BOND : bond 0.00084 ( 3) SS BOND : angle 0.73270 ( 6) hydrogen bonds : bond 0.03845 ( 437) hydrogen bonds : angle 4.65158 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6566 (mt0) cc_final: 0.6161 (mm-40) REVERT: A 216 LYS cc_start: 0.7026 (mptt) cc_final: 0.6728 (mmtt) REVERT: A 240 ASP cc_start: 0.7426 (p0) cc_final: 0.7192 (p0) REVERT: A 258 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7447 (mp0) REVERT: B 45 MET cc_start: 0.7697 (mtp) cc_final: 0.7173 (ttm) REVERT: B 68 ARG cc_start: 0.7453 (ttt180) cc_final: 0.7094 (ttt90) REVERT: B 137 ARG cc_start: 0.6648 (ttm-80) cc_final: 0.5793 (ttm-80) REVERT: B 220 GLN cc_start: 0.7272 (mt0) cc_final: 0.6942 (tt0) REVERT: B 263 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.6950 (m) REVERT: B 264 TYR cc_start: 0.7429 (m-80) cc_final: 0.6992 (m-80) REVERT: B 277 SER cc_start: 0.8578 (t) cc_final: 0.8187 (m) REVERT: B 322 ASP cc_start: 0.7468 (m-30) cc_final: 0.6810 (t0) REVERT: G 42 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7137 (mt-10) REVERT: N 46 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7012 (mt-10) REVERT: N 74 ASN cc_start: 0.7799 (m-40) cc_final: 0.7371 (m-40) REVERT: N 77 ASN cc_start: 0.6143 (t0) cc_final: 0.5889 (t0) REVERT: N 94 TYR cc_start: 0.8040 (m-80) cc_final: 0.7701 (m-80) REVERT: R 441 MET cc_start: 0.5981 (mmt) cc_final: 0.5679 (mmt) REVERT: R 465 GLU cc_start: 0.6007 (tp30) cc_final: 0.5754 (tp30) outliers start: 25 outliers final: 21 residues processed: 144 average time/residue: 0.0967 time to fit residues: 18.9839 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132975 restraints weight = 11268.650| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.09 r_work: 0.3503 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8687 Z= 0.124 Angle : 0.497 6.190 11813 Z= 0.270 Chirality : 0.041 0.159 1352 Planarity : 0.003 0.041 1514 Dihedral : 4.159 18.161 1215 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.74 % Allowed : 18.62 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.26), residues: 1113 helix: 1.39 (0.25), residues: 433 sheet: -0.41 (0.32), residues: 231 loop : -0.53 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.017 0.001 TYR R 191 PHE 0.031 0.002 PHE R 315 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8684) covalent geometry : angle 0.49708 (11807) SS BOND : bond 0.00058 ( 3) SS BOND : angle 0.68550 ( 6) hydrogen bonds : bond 0.03772 ( 437) hydrogen bonds : angle 4.53951 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6545 (mt0) cc_final: 0.6318 (mm-40) REVERT: A 216 LYS cc_start: 0.6959 (mptt) cc_final: 0.6582 (mmtt) REVERT: A 240 ASP cc_start: 0.7422 (p0) cc_final: 0.7210 (p0) REVERT: A 258 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7491 (mp0) REVERT: A 321 ASP cc_start: 0.7252 (m-30) cc_final: 0.7050 (m-30) REVERT: A 346 ARG cc_start: 0.6057 (mtt180) cc_final: 0.5811 (mmt-90) REVERT: B 45 MET cc_start: 0.7846 (mtp) cc_final: 0.7262 (ttm) REVERT: B 68 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7149 (ttt90) REVERT: B 137 ARG cc_start: 0.6639 (ttm-80) cc_final: 0.5801 (ttm-80) REVERT: B 220 GLN cc_start: 0.7312 (mt0) cc_final: 0.6954 (tt0) REVERT: B 263 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.6943 (m) REVERT: B 264 TYR cc_start: 0.7386 (m-80) cc_final: 0.7011 (m-80) REVERT: B 277 SER cc_start: 0.8573 (t) cc_final: 0.8191 (m) REVERT: B 322 ASP cc_start: 0.7370 (m-30) cc_final: 0.6712 (t0) REVERT: G 42 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7162 (mt-10) REVERT: N 46 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6991 (mt-10) REVERT: N 74 ASN cc_start: 0.7782 (m-40) cc_final: 0.7375 (m-40) REVERT: N 77 ASN cc_start: 0.6313 (t0) cc_final: 0.6027 (t0) REVERT: N 94 TYR cc_start: 0.8044 (m-80) cc_final: 0.7693 (m-80) REVERT: R 441 MET cc_start: 0.6017 (mmt) cc_final: 0.5688 (mmt) REVERT: R 465 GLU cc_start: 0.6042 (tp30) cc_final: 0.5787 (tp30) outliers start: 23 outliers final: 20 residues processed: 144 average time/residue: 0.0994 time to fit residues: 19.4666 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 0.0870 chunk 26 optimal weight: 0.1980 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133162 restraints weight = 11290.506| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.09 r_work: 0.3498 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8687 Z= 0.126 Angle : 0.503 6.611 11813 Z= 0.271 Chirality : 0.041 0.157 1352 Planarity : 0.003 0.042 1514 Dihedral : 4.120 17.525 1215 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.74 % Allowed : 18.97 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.26), residues: 1113 helix: 1.44 (0.25), residues: 433 sheet: -0.45 (0.32), residues: 226 loop : -0.51 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.018 0.001 TYR R 191 PHE 0.030 0.002 PHE R 315 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8684) covalent geometry : angle 0.50254 (11807) SS BOND : bond 0.00040 ( 3) SS BOND : angle 0.65922 ( 6) hydrogen bonds : bond 0.03766 ( 437) hydrogen bonds : angle 4.50013 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.44 seconds wall clock time: 41 minutes 48.25 seconds (2508.25 seconds total)