Starting phenix.real_space_refine on Sat Aug 23 06:36:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c60_16449/08_2025/8c60_16449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c60_16449/08_2025/8c60_16449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c60_16449/08_2025/8c60_16449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c60_16449/08_2025/8c60_16449.map" model { file = "/net/cci-nas-00/data/ceres_data/8c60_16449/08_2025/8c60_16449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c60_16449/08_2025/8c60_16449.cif" } resolution = 3.4 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= 0.002 sd= 0.032 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 S 71 5.16 5 C 6618 2.51 5 N 1791 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 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: 10393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 191} Chain breaks: 3 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8431 SG CYS C 289 37.156 60.679 44.363 1.00 98.27 S ATOM 8457 SG CYS C 292 34.484 59.125 42.002 1.00 76.90 S ATOM 8640 SG CYS C 315 38.214 58.340 41.438 1.00 99.87 S ATOM 8315 SG CYS C 274 37.578 47.560 46.382 1.00 76.54 S ATOM 8339 SG CYS C 277 38.854 43.874 45.997 1.00 76.10 S ATOM 8523 SG CYS C 300 41.127 46.197 47.023 1.00 52.30 S ATOM 7590 SG CYS C 71 45.057 96.067 75.745 1.00157.09 S ATOM 7614 SG CYS C 74 42.007 94.820 73.799 1.00171.24 S ATOM 7806 SG CYS C 99 44.586 97.004 72.093 1.00151.70 S ATOM 7833 SG CYS C 102 42.314 98.532 74.632 1.00154.53 S ATOM 7508 SG CYS C 59 47.178 87.777 66.516 1.00171.80 S ATOM 7528 SG CYS C 62 47.624 85.720 63.345 1.00149.40 S ATOM 7675 SG CYS C 82 49.675 88.925 63.768 1.00152.27 S Time building chain proxies: 2.56, per 1000 atoms: 0.25 Number of scatterers: 10393 At special positions: 0 Unit cell: (121.338, 127.008, 108.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 71 16.00 O 1906 8.00 N 1791 7.00 C 6618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.03 Conformation dependent library (CDL) restraints added in 390.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 99 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 102 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 74 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 71 " pdb=" ZN C1104 " pdb="ZN ZN C1104 " - pdb=" ND1 HIS C 79 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 62 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 59 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 82 " Number of angles added : 15 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 59.4% alpha, 5.1% 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 304 through 319 removed outlier: 3.722A pdb=" N PHE A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 340 through 353 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.673A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.088A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 Processing helix chain 'A' and resid 530 through 561 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.916A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.527A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.711A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.537A pdb=" N ARG A 792 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 814 through 829 Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.348A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 removed outlier: 3.518A pdb=" N LEU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 888 removed outlier: 3.662A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 5.169A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 33 through 46 removed outlier: 4.044A pdb=" N ARG B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.072A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.576A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.501A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.508A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 263 through 267 removed outlier: 4.038A pdb=" N SER B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 267 " --> pdb=" O ALA B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 267' Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.952A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.683A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.854A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.513A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.510A pdb=" N CYS C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 4.061A pdb=" N VAL C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.605A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 205 through 216 removed outlier: 3.786A pdb=" N ASP D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 249 through 266 removed outlier: 4.339A pdb=" N GLU D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 298 through 313 removed outlier: 3.925A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.741A pdb=" N ILE A 397 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.030A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.732A pdb=" N TYR B 14 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 258 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU B 299 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 260 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 171 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL B 197 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 173 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE B 199 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 175 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N LYS B 201 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'C' and resid 287 through 288 523 hydrogen bonds defined for protein. 1521 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: 1.67 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3402 1.34 - 1.46: 2277 1.46 - 1.58: 4842 1.58 - 1.70: 2 1.70 - 1.82: 104 Bond restraints: 10627 Sorted by residual: bond pdb=" CG LEU A 753 " pdb=" CD2 LEU A 753 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.84e+00 bond pdb=" C LYS D 204 " pdb=" N PRO D 205 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.24e+00 bond pdb=" CB PRO A 664 " pdb=" CG PRO A 664 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.69e+00 bond pdb=" CB PRO C 293 " pdb=" CG PRO C 293 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.51e+00 bond pdb=" C ALA D 299 " pdb=" N PRO D 300 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.44e-02 4.82e+03 3.14e+00 ... (remaining 10622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 14224 3.26 - 6.51: 107 6.51 - 9.77: 17 9.77 - 13.02: 3 13.02 - 16.28: 1 Bond angle restraints: 14352 Sorted by residual: angle pdb=" CA PRO A 664 " pdb=" N PRO A 664 " pdb=" CD PRO A 664 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.03e+01 angle pdb=" CA LEU A 347 " pdb=" CB LEU A 347 " pdb=" CG LEU A 347 " ideal model delta sigma weight residual 116.30 132.58 -16.28 3.50e+00 8.16e-02 2.16e+01 angle pdb=" C GLY D 298 " pdb=" N ALA D 299 " pdb=" CA ALA D 299 " ideal model delta sigma weight residual 120.09 125.59 -5.50 1.25e+00 6.40e-01 1.94e+01 angle pdb=" CA PRO C 293 " pdb=" N PRO C 293 " pdb=" CD PRO C 293 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" CG MET A 934 " pdb=" SD MET A 934 " pdb=" CE MET A 934 " ideal model delta sigma weight residual 100.90 92.53 8.37 2.20e+00 2.07e-01 1.45e+01 ... (remaining 14347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5443 17.29 - 34.59: 701 34.59 - 51.88: 248 51.88 - 69.18: 40 69.18 - 86.47: 17 Dihedral angle restraints: 6449 sinusoidal: 2681 harmonic: 3768 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LYS C 272 " pdb=" C LYS C 272 " pdb=" N VAL C 273 " pdb=" CA VAL C 273 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 16 " pdb=" C TYR B 16 " pdb=" N ASP B 17 " pdb=" CA ASP B 17 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1498 0.107 - 0.215: 33 0.215 - 0.322: 1 0.322 - 0.429: 1 0.429 - 0.537: 1 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CG LEU C 213 " pdb=" CB LEU C 213 " pdb=" CD1 LEU C 213 " pdb=" CD2 LEU C 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CG LEU C 355 " pdb=" CB LEU C 355 " pdb=" CD1 LEU C 355 " pdb=" CD2 LEU C 355 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU D 213 " pdb=" CB LEU D 213 " pdb=" CD1 LEU D 213 " pdb=" CD2 LEU D 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1531 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 663 " 0.079 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 664 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 292 " -0.054 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO C 293 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 293 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 293 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 315 " -0.198 9.50e-02 1.11e+02 8.93e-02 6.15e+00 pdb=" NE ARG A 315 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 315 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 315 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 315 " -0.014 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 33 2.38 - 3.01: 5937 3.01 - 3.64: 16128 3.64 - 4.27: 23576 4.27 - 4.90: 39100 Nonbonded interactions: 84774 Sorted by model distance: nonbonded pdb=" CG HIS B 179 " pdb="ZN ZN B 501 " model vdw 1.750 1.960 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 501 " model vdw 2.136 2.230 nonbonded pdb=" ND2 ASN B 96 " pdb=" O ALA B 148 " model vdw 2.183 3.120 nonbonded pdb=" OG1 THR C 330 " pdb=" OD1 ASN C 333 " model vdw 2.249 3.040 nonbonded pdb=" O ASN D 228 " pdb=" OG SER D 231 " model vdw 2.265 3.040 ... (remaining 84769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 10644 Z= 0.164 Angle : 0.797 16.990 14367 Z= 0.406 Chirality : 0.047 0.537 1534 Planarity : 0.006 0.114 1862 Dihedral : 17.712 86.471 4015 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.80 % Allowed : 29.15 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: -0.10 (0.24), residues: 1260 helix: 0.70 (0.20), residues: 671 sheet: -0.50 (0.63), residues: 74 loop : -0.95 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 315 TYR 0.036 0.002 TYR D 236 PHE 0.031 0.002 PHE A 743 TRP 0.039 0.002 TRP A 560 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00372 (10627) covalent geometry : angle 0.78346 (14352) hydrogen bonds : bond 0.13965 ( 523) hydrogen bonds : angle 6.04310 ( 1521) metal coordination : bond 0.01875 ( 17) metal coordination : angle 4.64279 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 279 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 LYS cc_start: 0.7588 (tptt) cc_final: 0.7081 (tptm) REVERT: A 557 ASN cc_start: 0.7745 (t0) cc_final: 0.7510 (t0) REVERT: A 570 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8064 (ttpp) REVERT: A 625 GLU cc_start: 0.6413 (pm20) cc_final: 0.5180 (pm20) REVERT: A 771 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7605 (mt0) REVERT: A 776 GLU cc_start: 0.7120 (tp30) cc_final: 0.6706 (tp30) REVERT: A 822 MET cc_start: 0.7800 (ttm) cc_final: 0.7546 (ttm) REVERT: A 843 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7547 (mpp) REVERT: A 922 LYS cc_start: 0.8008 (tmmt) cc_final: 0.7781 (tmmt) REVERT: B 75 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7247 (mmmt) REVERT: B 265 ASP cc_start: 0.6929 (p0) cc_final: 0.6625 (p0) REVERT: B 327 ASN cc_start: 0.8291 (t0) cc_final: 0.7981 (t0) outliers start: 9 outliers final: 1 residues processed: 281 average time/residue: 0.1250 time to fit residues: 47.5359 Evaluate side-chains 272 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 843 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 123 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN A 574 HIS ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.174687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146737 restraints weight = 16293.164| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.72 r_work: 0.3723 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10644 Z= 0.179 Angle : 0.679 16.626 14367 Z= 0.334 Chirality : 0.045 0.306 1534 Planarity : 0.005 0.072 1862 Dihedral : 4.388 24.030 1413 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.80 % Allowed : 24.20 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.22 (0.24), residues: 1260 helix: 1.04 (0.20), residues: 683 sheet: -0.58 (0.62), residues: 75 loop : -0.94 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 762 TYR 0.029 0.002 TYR D 329 PHE 0.026 0.002 PHE A 362 TRP 0.019 0.002 TRP D 206 HIS 0.009 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00393 (10627) covalent geometry : angle 0.66164 (14352) hydrogen bonds : bond 0.04232 ( 523) hydrogen bonds : angle 4.69477 ( 1521) metal coordination : bond 0.00809 ( 17) metal coordination : angle 4.76551 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.7532 (m-80) cc_final: 0.7073 (m-10) REVERT: A 457 ASP cc_start: 0.7429 (m-30) cc_final: 0.7159 (m-30) REVERT: A 458 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 503 THR cc_start: 0.7930 (p) cc_final: 0.7697 (m) REVERT: A 515 ILE cc_start: 0.7463 (mm) cc_final: 0.7240 (mm) REVERT: A 522 GLU cc_start: 0.7351 (mp0) cc_final: 0.7028 (mp0) REVERT: A 545 LYS cc_start: 0.7722 (tptt) cc_final: 0.7145 (tppt) REVERT: A 557 ASN cc_start: 0.7743 (t160) cc_final: 0.7484 (t0) REVERT: A 582 ASN cc_start: 0.7311 (m-40) cc_final: 0.7003 (m-40) REVERT: A 601 ASP cc_start: 0.6659 (m-30) cc_final: 0.6441 (m-30) REVERT: A 741 SER cc_start: 0.8214 (t) cc_final: 0.7596 (p) REVERT: A 787 LEU cc_start: 0.4303 (OUTLIER) cc_final: 0.4062 (tt) REVERT: A 835 GLN cc_start: 0.7537 (mp10) cc_final: 0.7331 (mp10) REVERT: A 857 LEU cc_start: 0.7501 (tp) cc_final: 0.7248 (tp) REVERT: A 922 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7717 (tmmt) REVERT: A 925 PHE cc_start: 0.7746 (m-80) cc_final: 0.7400 (m-80) REVERT: B 44 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6042 (mp) REVERT: B 75 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7299 (mttp) REVERT: B 127 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7184 (mpp80) REVERT: B 132 MET cc_start: 0.7453 (ttm) cc_final: 0.7251 (ttt) REVERT: B 146 SER cc_start: 0.8443 (m) cc_final: 0.8173 (t) REVERT: B 151 PHE cc_start: 0.8551 (m-10) cc_final: 0.8085 (m-80) REVERT: B 243 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7777 (ttpt) REVERT: B 265 ASP cc_start: 0.7235 (p0) cc_final: 0.6803 (p0) REVERT: B 327 ASN cc_start: 0.8318 (t0) cc_final: 0.7992 (t0) REVERT: B 336 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 20 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7294 (tp) REVERT: C 298 MET cc_start: 0.8086 (mmm) cc_final: 0.7819 (mmt) REVERT: C 305 LEU cc_start: 0.8169 (mt) cc_final: 0.7915 (mp) REVERT: D 303 LEU cc_start: 0.7807 (tp) cc_final: 0.7550 (tp) outliers start: 43 outliers final: 17 residues processed: 328 average time/residue: 0.1283 time to fit residues: 56.1032 Evaluate side-chains 298 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.0770 chunk 117 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 606 GLN A 607 HIS ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146038 restraints weight = 16173.678| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.58 r_work: 0.3719 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10644 Z= 0.156 Angle : 0.651 16.080 14367 Z= 0.315 Chirality : 0.043 0.232 1534 Planarity : 0.004 0.051 1862 Dihedral : 4.207 22.840 1408 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.53 % Allowed : 26.15 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.41 (0.24), residues: 1260 helix: 1.24 (0.20), residues: 676 sheet: -0.68 (0.61), residues: 75 loop : -0.86 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 768 TYR 0.024 0.002 TYR D 329 PHE 0.016 0.002 PHE A 743 TRP 0.017 0.002 TRP A 560 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00351 (10627) covalent geometry : angle 0.63508 (14352) hydrogen bonds : bond 0.04011 ( 523) hydrogen bonds : angle 4.60713 ( 1521) metal coordination : bond 0.00865 ( 17) metal coordination : angle 4.52256 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.5132 (mttt) cc_final: 0.3760 (ptpt) REVERT: A 457 ASP cc_start: 0.7365 (m-30) cc_final: 0.7002 (m-30) REVERT: A 458 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6876 (mt-10) REVERT: A 463 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6886 (t0) REVERT: A 470 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8097 (mm) REVERT: A 475 VAL cc_start: 0.8004 (t) cc_final: 0.7782 (p) REVERT: A 522 GLU cc_start: 0.7278 (mp0) cc_final: 0.7046 (mp0) REVERT: A 557 ASN cc_start: 0.7759 (t160) cc_final: 0.7533 (t0) REVERT: A 601 ASP cc_start: 0.6682 (m-30) cc_final: 0.6444 (m-30) REVERT: A 741 SER cc_start: 0.8270 (t) cc_final: 0.7610 (p) REVERT: A 787 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.4049 (tt) REVERT: A 822 MET cc_start: 0.7818 (ttm) cc_final: 0.7367 (ttm) REVERT: A 835 GLN cc_start: 0.7458 (mp10) cc_final: 0.7183 (mp10) REVERT: A 857 LEU cc_start: 0.7759 (tp) cc_final: 0.7488 (tp) REVERT: A 925 PHE cc_start: 0.7899 (m-80) cc_final: 0.7458 (m-80) REVERT: B 44 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5895 (mp) REVERT: B 75 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7341 (mtmm) REVERT: B 91 GLN cc_start: 0.8221 (mt0) cc_final: 0.7992 (mt0) REVERT: B 127 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7169 (mpp80) REVERT: B 132 MET cc_start: 0.7378 (ttm) cc_final: 0.7152 (ttt) REVERT: B 151 PHE cc_start: 0.8555 (m-10) cc_final: 0.8098 (m-80) REVERT: B 155 ASN cc_start: 0.8174 (t0) cc_final: 0.7896 (t0) REVERT: B 211 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6719 (m-30) REVERT: B 236 GLU cc_start: 0.6356 (pm20) cc_final: 0.6134 (pm20) REVERT: B 265 ASP cc_start: 0.7432 (p0) cc_final: 0.7084 (p0) REVERT: C 20 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7107 (tp) REVERT: C 91 MET cc_start: 0.5271 (tpt) cc_final: 0.5048 (tpt) REVERT: C 286 LEU cc_start: 0.8314 (mt) cc_final: 0.8097 (mm) REVERT: C 305 LEU cc_start: 0.8173 (mt) cc_final: 0.7913 (mp) REVERT: D 206 TRP cc_start: 0.8560 (t-100) cc_final: 0.8347 (t-100) REVERT: D 265 ASN cc_start: 0.6894 (OUTLIER) cc_final: 0.6681 (m110) REVERT: D 303 LEU cc_start: 0.7815 (tp) cc_final: 0.7546 (tp) outliers start: 40 outliers final: 15 residues processed: 310 average time/residue: 0.1170 time to fit residues: 48.9959 Evaluate side-chains 302 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 607 HIS Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 265 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 0.0470 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 20 optimal weight: 0.0030 chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 574 HIS ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.172391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145262 restraints weight = 16274.403| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.56 r_work: 0.3704 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10644 Z= 0.138 Angle : 0.625 15.816 14367 Z= 0.305 Chirality : 0.042 0.209 1534 Planarity : 0.004 0.050 1862 Dihedral : 4.132 20.891 1408 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.27 % Allowed : 26.94 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.40 (0.20), residues: 667 sheet: -0.64 (0.62), residues: 75 loop : -0.87 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.023 0.001 TYR D 329 PHE 0.023 0.002 PHE B 188 TRP 0.015 0.001 TRP A 560 HIS 0.013 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00310 (10627) covalent geometry : angle 0.60872 (14352) hydrogen bonds : bond 0.03720 ( 523) hydrogen bonds : angle 4.50491 ( 1521) metal coordination : bond 0.00911 ( 17) metal coordination : angle 4.41677 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 VAL cc_start: 0.7093 (OUTLIER) cc_final: 0.6700 (t) REVERT: A 444 LYS cc_start: 0.5243 (mttt) cc_final: 0.3956 (ptpt) REVERT: A 457 ASP cc_start: 0.7373 (m-30) cc_final: 0.6961 (m-30) REVERT: A 458 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7045 (mt-10) REVERT: A 470 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 522 GLU cc_start: 0.7388 (mp0) cc_final: 0.7107 (mp0) REVERT: A 546 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6943 (tm-30) REVERT: A 580 LYS cc_start: 0.8282 (mmmm) cc_final: 0.7829 (mtmm) REVERT: A 601 ASP cc_start: 0.6787 (m-30) cc_final: 0.6555 (m-30) REVERT: A 741 SER cc_start: 0.8276 (t) cc_final: 0.7582 (p) REVERT: A 787 LEU cc_start: 0.4429 (OUTLIER) cc_final: 0.4202 (tt) REVERT: A 822 MET cc_start: 0.7765 (ttm) cc_final: 0.7371 (ttm) REVERT: A 835 GLN cc_start: 0.7443 (mp10) cc_final: 0.7111 (mp10) REVERT: A 842 GLU cc_start: 0.7707 (pp20) cc_final: 0.7402 (tp30) REVERT: A 855 ASP cc_start: 0.6988 (p0) cc_final: 0.6704 (p0) REVERT: A 857 LEU cc_start: 0.7764 (tp) cc_final: 0.7478 (tp) REVERT: A 925 PHE cc_start: 0.7937 (m-80) cc_final: 0.7431 (m-80) REVERT: A 935 THR cc_start: 0.8035 (m) cc_final: 0.7520 (t) REVERT: B 44 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.6001 (mp) REVERT: B 75 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7393 (mtmm) REVERT: B 91 GLN cc_start: 0.8211 (mt0) cc_final: 0.7958 (mt0) REVERT: B 92 MET cc_start: 0.8525 (ttt) cc_final: 0.8125 (ttm) REVERT: B 95 PHE cc_start: 0.8410 (m-10) cc_final: 0.8179 (m-80) REVERT: B 100 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 127 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7169 (mpp80) REVERT: B 146 SER cc_start: 0.8503 (t) cc_final: 0.8213 (t) REVERT: B 151 PHE cc_start: 0.8553 (m-10) cc_final: 0.8153 (m-80) REVERT: B 155 ASN cc_start: 0.8149 (t0) cc_final: 0.7843 (t0) REVERT: B 236 GLU cc_start: 0.6291 (pm20) cc_final: 0.6072 (pm20) REVERT: B 243 LYS cc_start: 0.8056 (tttp) cc_final: 0.7809 (ttpt) REVERT: B 265 ASP cc_start: 0.7724 (p0) cc_final: 0.7424 (p0) REVERT: B 327 ASN cc_start: 0.8240 (t0) cc_final: 0.8019 (t0) REVERT: C 21 MET cc_start: 0.8396 (mmm) cc_final: 0.7581 (mmm) REVERT: C 91 MET cc_start: 0.5306 (tpt) cc_final: 0.5077 (tpt) REVERT: C 272 LYS cc_start: 0.7016 (pttt) cc_final: 0.6813 (pttt) REVERT: D 206 TRP cc_start: 0.8601 (t-100) cc_final: 0.8373 (t-100) REVERT: D 303 LEU cc_start: 0.7834 (tp) cc_final: 0.7571 (tp) outliers start: 37 outliers final: 19 residues processed: 305 average time/residue: 0.1272 time to fit residues: 52.1111 Evaluate side-chains 310 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.169395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141799 restraints weight = 16238.021| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.57 r_work: 0.3662 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10644 Z= 0.161 Angle : 0.636 16.432 14367 Z= 0.313 Chirality : 0.043 0.213 1534 Planarity : 0.004 0.049 1862 Dihedral : 4.164 21.554 1408 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.98 % Allowed : 26.06 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1260 helix: 1.27 (0.20), residues: 679 sheet: -0.46 (0.62), residues: 74 loop : -0.89 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 193 TYR 0.023 0.002 TYR D 329 PHE 0.020 0.002 PHE A 355 TRP 0.013 0.001 TRP A 560 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00361 (10627) covalent geometry : angle 0.61897 (14352) hydrogen bonds : bond 0.03754 ( 523) hydrogen bonds : angle 4.52676 ( 1521) metal coordination : bond 0.00900 ( 17) metal coordination : angle 4.54193 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6834 (p) REVERT: A 315 ARG cc_start: 0.6959 (mmm160) cc_final: 0.6567 (mmp-170) REVERT: A 327 PHE cc_start: 0.8316 (t80) cc_final: 0.8051 (t80) REVERT: A 428 TRP cc_start: 0.8572 (m100) cc_final: 0.7888 (m100) REVERT: A 444 LYS cc_start: 0.5341 (mttt) cc_final: 0.3926 (ptpt) REVERT: A 456 GLU cc_start: 0.7639 (tp30) cc_final: 0.7287 (tp30) REVERT: A 457 ASP cc_start: 0.7523 (m-30) cc_final: 0.6741 (m-30) REVERT: A 458 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7093 (mt-10) REVERT: A 470 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8213 (mm) REVERT: A 519 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7507 (mtmm) REVERT: A 522 GLU cc_start: 0.7386 (mp0) cc_final: 0.7144 (mp0) REVERT: A 546 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 559 ILE cc_start: 0.7500 (mt) cc_final: 0.7087 (mt) REVERT: A 580 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7836 (mtmm) REVERT: A 597 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 601 ASP cc_start: 0.7059 (m-30) cc_final: 0.6743 (m-30) REVERT: A 602 GLU cc_start: 0.7213 (tt0) cc_final: 0.6890 (tt0) REVERT: A 776 GLU cc_start: 0.7373 (tp30) cc_final: 0.7019 (tp30) REVERT: A 787 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4231 (tt) REVERT: A 822 MET cc_start: 0.7836 (ttm) cc_final: 0.7374 (ttm) REVERT: A 832 ASP cc_start: 0.7764 (t0) cc_final: 0.7299 (t0) REVERT: A 835 GLN cc_start: 0.7461 (mp10) cc_final: 0.7085 (mp10) REVERT: A 855 ASP cc_start: 0.7226 (p0) cc_final: 0.6794 (p0) REVERT: A 856 LYS cc_start: 0.7790 (mttm) cc_final: 0.7383 (mptt) REVERT: A 915 MET cc_start: 0.6408 (mpp) cc_final: 0.5949 (mpp) REVERT: A 925 PHE cc_start: 0.8066 (m-80) cc_final: 0.7758 (m-80) REVERT: A 935 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7684 (t) REVERT: B 44 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6309 (mp) REVERT: B 49 TYR cc_start: 0.6402 (p90) cc_final: 0.6186 (p90) REVERT: B 75 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7396 (mttp) REVERT: B 91 GLN cc_start: 0.8209 (mt0) cc_final: 0.7948 (mt0) REVERT: B 92 MET cc_start: 0.8520 (ttt) cc_final: 0.8139 (ttm) REVERT: B 100 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7443 (t0) REVERT: B 124 LYS cc_start: 0.7229 (ttpt) cc_final: 0.7023 (mtpt) REVERT: B 127 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7281 (mpp80) REVERT: B 146 SER cc_start: 0.8662 (t) cc_final: 0.8374 (t) REVERT: B 155 ASN cc_start: 0.8274 (t0) cc_final: 0.8019 (t0) REVERT: B 236 GLU cc_start: 0.6428 (pm20) cc_final: 0.6214 (pm20) REVERT: B 265 ASP cc_start: 0.8086 (p0) cc_final: 0.7881 (p0) REVERT: B 271 ARG cc_start: 0.8236 (ttt90) cc_final: 0.8015 (ttm-80) REVERT: B 294 LEU cc_start: 0.8564 (mp) cc_final: 0.8306 (mt) REVERT: C 21 MET cc_start: 0.8437 (mmm) cc_final: 0.7572 (mmm) REVERT: C 91 MET cc_start: 0.5389 (tpt) cc_final: 0.5047 (tpt) REVERT: C 272 LYS cc_start: 0.7286 (pttt) cc_final: 0.7015 (pttt) REVERT: C 279 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8039 (mtp-110) REVERT: C 329 MET cc_start: 0.6614 (tpp) cc_final: 0.6215 (mpp) REVERT: D 206 TRP cc_start: 0.8643 (t-100) cc_final: 0.8370 (t-100) REVERT: D 261 LYS cc_start: 0.8287 (mttm) cc_final: 0.7675 (mttm) REVERT: D 265 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6540 (m110) outliers start: 45 outliers final: 20 residues processed: 322 average time/residue: 0.1298 time to fit residues: 56.0264 Evaluate side-chains 313 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 771 GLN B 45 ASN B 112 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN C 25 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.169840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141164 restraints weight = 16454.379| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.65 r_work: 0.3663 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10644 Z= 0.164 Angle : 0.648 16.506 14367 Z= 0.316 Chirality : 0.043 0.222 1534 Planarity : 0.004 0.049 1862 Dihedral : 4.205 21.918 1408 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.89 % Allowed : 27.47 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.42 (0.24), residues: 1260 helix: 1.23 (0.20), residues: 677 sheet: -0.38 (0.61), residues: 74 loop : -0.89 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 768 TYR 0.025 0.002 TYR D 329 PHE 0.028 0.002 PHE A 743 TRP 0.011 0.002 TRP C 97 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00369 (10627) covalent geometry : angle 0.63030 (14352) hydrogen bonds : bond 0.03735 ( 523) hydrogen bonds : angle 4.55175 ( 1521) metal coordination : bond 0.00929 ( 17) metal coordination : angle 4.68900 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6846 (mmm160) cc_final: 0.6478 (mmm160) REVERT: A 327 PHE cc_start: 0.8337 (t80) cc_final: 0.8060 (t80) REVERT: A 428 TRP cc_start: 0.8581 (m100) cc_final: 0.7972 (m100) REVERT: A 456 GLU cc_start: 0.7638 (tp30) cc_final: 0.7289 (tp30) REVERT: A 457 ASP cc_start: 0.7566 (m-30) cc_final: 0.6645 (m-30) REVERT: A 458 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7096 (mt-10) REVERT: A 470 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8270 (mm) REVERT: A 505 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 522 GLU cc_start: 0.7368 (mp0) cc_final: 0.7118 (mp0) REVERT: A 546 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 597 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 601 ASP cc_start: 0.7078 (m-30) cc_final: 0.6781 (m-30) REVERT: A 602 GLU cc_start: 0.7260 (tt0) cc_final: 0.6998 (tt0) REVERT: A 625 GLU cc_start: 0.6933 (pm20) cc_final: 0.6639 (pm20) REVERT: A 768 ARG cc_start: 0.7513 (mpt-90) cc_final: 0.7228 (mpt-90) REVERT: A 772 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8258 (ttmm) REVERT: A 776 GLU cc_start: 0.7396 (tp30) cc_final: 0.7029 (tp30) REVERT: A 787 LEU cc_start: 0.4469 (OUTLIER) cc_final: 0.4232 (tt) REVERT: A 822 MET cc_start: 0.7807 (ttm) cc_final: 0.7392 (ttm) REVERT: A 835 GLN cc_start: 0.7358 (mp10) cc_final: 0.7017 (mp10) REVERT: A 854 MET cc_start: 0.8524 (mmm) cc_final: 0.8182 (mmt) REVERT: A 855 ASP cc_start: 0.7457 (p0) cc_final: 0.7074 (p0) REVERT: A 856 LYS cc_start: 0.7962 (mttm) cc_final: 0.7561 (mptt) REVERT: A 863 ARG cc_start: 0.7332 (ttp-110) cc_final: 0.7069 (ttm-80) REVERT: A 915 MET cc_start: 0.6429 (mpp) cc_final: 0.6182 (mpp) REVERT: A 935 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7794 (t) REVERT: B 49 TYR cc_start: 0.6448 (p90) cc_final: 0.6231 (p90) REVERT: B 74 ILE cc_start: 0.7532 (mm) cc_final: 0.7275 (mm) REVERT: B 75 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7467 (mttp) REVERT: B 91 GLN cc_start: 0.8243 (mt0) cc_final: 0.7989 (mt0) REVERT: B 92 MET cc_start: 0.8468 (ttt) cc_final: 0.8095 (ttm) REVERT: B 100 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7439 (t0) REVERT: B 127 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7321 (mpp80) REVERT: B 144 LYS cc_start: 0.8534 (mmtp) cc_final: 0.8296 (mmtp) REVERT: B 146 SER cc_start: 0.8788 (t) cc_final: 0.8509 (t) REVERT: B 155 ASN cc_start: 0.8270 (t0) cc_final: 0.7927 (t0) REVERT: B 156 ASP cc_start: 0.7672 (p0) cc_final: 0.7332 (p0) REVERT: B 236 GLU cc_start: 0.6470 (pm20) cc_final: 0.6195 (pm20) REVERT: B 271 ARG cc_start: 0.8258 (ttt90) cc_final: 0.8014 (ttm-80) REVERT: B 294 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 366 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.7361 (ttt180) REVERT: C 21 MET cc_start: 0.8463 (mmm) cc_final: 0.7715 (mmm) REVERT: C 91 MET cc_start: 0.5382 (tpt) cc_final: 0.5027 (tpt) REVERT: C 272 LYS cc_start: 0.7490 (pttt) cc_final: 0.7243 (pttt) REVERT: C 279 ARG cc_start: 0.8568 (mtp-110) cc_final: 0.8199 (mtm110) REVERT: C 329 MET cc_start: 0.6655 (tpp) cc_final: 0.6241 (mpp) REVERT: D 206 TRP cc_start: 0.8562 (t-100) cc_final: 0.8286 (t-100) REVERT: D 261 LYS cc_start: 0.8218 (mttm) cc_final: 0.7599 (mttm) REVERT: D 265 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6613 (m-40) outliers start: 44 outliers final: 20 residues processed: 330 average time/residue: 0.1310 time to fit residues: 58.0394 Evaluate side-chains 324 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 773 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 142 HIS B 261 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.168694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140245 restraints weight = 16229.744| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.58 r_work: 0.3649 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10644 Z= 0.169 Angle : 0.663 16.590 14367 Z= 0.327 Chirality : 0.043 0.224 1534 Planarity : 0.004 0.048 1862 Dihedral : 4.290 22.454 1408 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.71 % Allowed : 27.03 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.43 (0.24), residues: 1260 helix: 1.15 (0.20), residues: 686 sheet: -0.38 (0.60), residues: 74 loop : -0.77 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 643 TYR 0.025 0.002 TYR D 329 PHE 0.022 0.002 PHE A 743 TRP 0.010 0.001 TRP C 313 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00384 (10627) covalent geometry : angle 0.64585 (14352) hydrogen bonds : bond 0.03792 ( 523) hydrogen bonds : angle 4.52174 ( 1521) metal coordination : bond 0.00987 ( 17) metal coordination : angle 4.63217 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7323 (mm) REVERT: A 428 TRP cc_start: 0.8589 (m100) cc_final: 0.7981 (m100) REVERT: A 457 ASP cc_start: 0.7687 (m-30) cc_final: 0.7079 (m-30) REVERT: A 458 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 461 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6757 (tp30) REVERT: A 463 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.6928 (t0) REVERT: A 470 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 492 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5280 (pm20) REVERT: A 493 LYS cc_start: 0.7532 (tptp) cc_final: 0.7328 (tptp) REVERT: A 505 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 522 GLU cc_start: 0.7449 (mp0) cc_final: 0.7249 (mp0) REVERT: A 546 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 597 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 601 ASP cc_start: 0.7209 (m-30) cc_final: 0.6919 (m-30) REVERT: A 625 GLU cc_start: 0.6887 (pm20) cc_final: 0.6642 (pm20) REVERT: A 752 PHE cc_start: 0.7958 (t80) cc_final: 0.7492 (t80) REVERT: A 768 ARG cc_start: 0.7680 (mpt-90) cc_final: 0.7420 (mpt-90) REVERT: A 776 GLU cc_start: 0.7335 (tp30) cc_final: 0.6971 (tp30) REVERT: A 787 LEU cc_start: 0.4384 (OUTLIER) cc_final: 0.4176 (tt) REVERT: A 822 MET cc_start: 0.7724 (ttm) cc_final: 0.7291 (ttm) REVERT: A 835 GLN cc_start: 0.7308 (mp10) cc_final: 0.7069 (mp10) REVERT: A 854 MET cc_start: 0.8489 (mmm) cc_final: 0.8273 (mmt) REVERT: A 855 ASP cc_start: 0.7555 (p0) cc_final: 0.7147 (p0) REVERT: A 856 LYS cc_start: 0.8072 (mttm) cc_final: 0.7670 (mptt) REVERT: A 863 ARG cc_start: 0.7379 (ttp-110) cc_final: 0.7099 (ttm-80) REVERT: A 904 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7647 (pp20) REVERT: A 935 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7798 (t) REVERT: B 74 ILE cc_start: 0.7567 (mm) cc_final: 0.7336 (mm) REVERT: B 75 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7531 (mttp) REVERT: B 91 GLN cc_start: 0.8177 (mt0) cc_final: 0.7931 (mt0) REVERT: B 92 MET cc_start: 0.8481 (ttt) cc_final: 0.8115 (ttm) REVERT: B 100 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7504 (t70) REVERT: B 127 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7368 (mpp80) REVERT: B 144 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8271 (mmtp) REVERT: B 146 SER cc_start: 0.8836 (t) cc_final: 0.8569 (t) REVERT: B 155 ASN cc_start: 0.8321 (t0) cc_final: 0.8006 (t0) REVERT: B 156 ASP cc_start: 0.7644 (p0) cc_final: 0.7327 (p0) REVERT: B 236 GLU cc_start: 0.6532 (pm20) cc_final: 0.6243 (pm20) REVERT: B 248 LYS cc_start: 0.7440 (tppt) cc_final: 0.7068 (tppt) REVERT: B 265 ASP cc_start: 0.7700 (p0) cc_final: 0.7491 (p0) REVERT: B 360 MET cc_start: 0.7928 (mmm) cc_final: 0.7516 (tpp) REVERT: B 366 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7457 (ttt180) REVERT: B 372 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6328 (mmt180) REVERT: C 21 MET cc_start: 0.8470 (mmm) cc_final: 0.7732 (mmm) REVERT: C 91 MET cc_start: 0.5424 (tpt) cc_final: 0.5043 (tpt) REVERT: C 316 PRO cc_start: 0.8460 (Cg_endo) cc_final: 0.8233 (Cg_exo) REVERT: C 329 MET cc_start: 0.6698 (tpp) cc_final: 0.6285 (mpp) REVERT: D 206 TRP cc_start: 0.8521 (t-100) cc_final: 0.8241 (t-100) outliers start: 42 outliers final: 26 residues processed: 329 average time/residue: 0.1195 time to fit residues: 53.5982 Evaluate side-chains 332 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 295 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 261 GLN C 25 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.170831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142662 restraints weight = 16220.506| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.59 r_work: 0.3686 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10644 Z= 0.126 Angle : 0.656 15.403 14367 Z= 0.320 Chirality : 0.042 0.208 1534 Planarity : 0.004 0.048 1862 Dihedral : 4.176 20.998 1408 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.27 % Allowed : 27.74 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.36 (0.20), residues: 673 sheet: -0.44 (0.61), residues: 75 loop : -0.77 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 643 TYR 0.024 0.001 TYR D 329 PHE 0.029 0.001 PHE A 362 TRP 0.010 0.001 TRP C 313 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00283 (10627) covalent geometry : angle 0.63991 (14352) hydrogen bonds : bond 0.03588 ( 523) hydrogen bonds : angle 4.44311 ( 1521) metal coordination : bond 0.01318 ( 17) metal coordination : angle 4.44873 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ASN cc_start: 0.6753 (m-40) cc_final: 0.6548 (m-40) REVERT: A 328 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 444 LYS cc_start: 0.5348 (mttt) cc_final: 0.3803 (ptpt) REVERT: A 457 ASP cc_start: 0.7565 (m-30) cc_final: 0.6763 (m-30) REVERT: A 458 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 470 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (mm) REVERT: A 493 LYS cc_start: 0.7553 (tptp) cc_final: 0.7309 (tptp) REVERT: A 505 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 522 GLU cc_start: 0.7474 (mp0) cc_final: 0.7247 (mp0) REVERT: A 546 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 596 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 597 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 601 ASP cc_start: 0.7174 (m-30) cc_final: 0.6901 (m-30) REVERT: A 625 GLU cc_start: 0.6929 (pm20) cc_final: 0.6662 (pm20) REVERT: A 667 PHE cc_start: 0.5964 (m-80) cc_final: 0.5679 (m-80) REVERT: A 752 PHE cc_start: 0.7992 (t80) cc_final: 0.7523 (t80) REVERT: A 776 GLU cc_start: 0.7351 (tp30) cc_final: 0.6979 (tp30) REVERT: A 787 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.4187 (tt) REVERT: A 822 MET cc_start: 0.7661 (ttm) cc_final: 0.7266 (ttm) REVERT: A 855 ASP cc_start: 0.7562 (p0) cc_final: 0.7144 (p0) REVERT: A 856 LYS cc_start: 0.8005 (mttm) cc_final: 0.7651 (mptt) REVERT: A 863 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7102 (ttm-80) REVERT: A 904 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7671 (pp20) REVERT: A 935 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7758 (p) REVERT: B 32 LYS cc_start: 0.8605 (mttm) cc_final: 0.8383 (mttp) REVERT: B 65 MET cc_start: 0.8113 (mtt) cc_final: 0.7645 (mtt) REVERT: B 75 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7484 (mttp) REVERT: B 91 GLN cc_start: 0.8157 (mt0) cc_final: 0.7945 (mt0) REVERT: B 92 MET cc_start: 0.8494 (ttt) cc_final: 0.8175 (ttm) REVERT: B 127 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7311 (mpp80) REVERT: B 144 LYS cc_start: 0.8526 (mmtp) cc_final: 0.8128 (mmtt) REVERT: B 155 ASN cc_start: 0.8244 (t0) cc_final: 0.7909 (t0) REVERT: B 156 ASP cc_start: 0.7644 (p0) cc_final: 0.7314 (p0) REVERT: B 236 GLU cc_start: 0.6517 (pm20) cc_final: 0.6217 (pm20) REVERT: B 248 LYS cc_start: 0.7236 (tppt) cc_final: 0.7000 (tppt) REVERT: B 265 ASP cc_start: 0.7391 (p0) cc_final: 0.7169 (p0) REVERT: B 360 MET cc_start: 0.7846 (mmm) cc_final: 0.7419 (tpp) REVERT: B 372 ARG cc_start: 0.7099 (mmt180) cc_final: 0.6305 (mmt180) REVERT: C 21 MET cc_start: 0.8445 (mmm) cc_final: 0.7989 (mmm) REVERT: C 91 MET cc_start: 0.5514 (tpt) cc_final: 0.5111 (tpt) REVERT: C 266 LEU cc_start: 0.7646 (tp) cc_final: 0.7404 (tt) REVERT: C 272 LYS cc_start: 0.7525 (pttt) cc_final: 0.7287 (pttt) REVERT: C 329 MET cc_start: 0.6657 (tpp) cc_final: 0.6244 (mpp) REVERT: D 206 TRP cc_start: 0.8488 (t-100) cc_final: 0.8190 (t-100) outliers start: 37 outliers final: 24 residues processed: 317 average time/residue: 0.1229 time to fit residues: 52.9364 Evaluate side-chains 320 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 337 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 100 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 261 GLN C 25 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141953 restraints weight = 16110.773| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.59 r_work: 0.3689 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10644 Z= 0.135 Angle : 0.669 14.305 14367 Z= 0.327 Chirality : 0.043 0.219 1534 Planarity : 0.004 0.053 1862 Dihedral : 4.221 24.990 1408 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.36 % Allowed : 28.27 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.27 (0.20), residues: 691 sheet: -0.46 (0.61), residues: 74 loop : -0.79 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 768 TYR 0.026 0.001 TYR B 304 PHE 0.020 0.001 PHE A 743 TRP 0.012 0.001 TRP A 428 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00308 (10627) covalent geometry : angle 0.65334 (14352) hydrogen bonds : bond 0.03593 ( 523) hydrogen bonds : angle 4.43082 ( 1521) metal coordination : bond 0.00971 ( 17) metal coordination : angle 4.52108 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6560 (t) REVERT: A 326 ASN cc_start: 0.6815 (m-40) cc_final: 0.6612 (m-40) REVERT: A 328 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 402 ARG cc_start: 0.7406 (ptp90) cc_final: 0.7189 (ptt180) REVERT: A 444 LYS cc_start: 0.5348 (mttt) cc_final: 0.3646 (ptpt) REVERT: A 457 ASP cc_start: 0.7558 (m-30) cc_final: 0.6931 (m-30) REVERT: A 470 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 492 GLU cc_start: 0.5661 (OUTLIER) cc_final: 0.5209 (pm20) REVERT: A 493 LYS cc_start: 0.7558 (tptp) cc_final: 0.7305 (tptp) REVERT: A 505 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 546 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 570 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7986 (ttmt) REVERT: A 596 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 597 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 601 ASP cc_start: 0.7211 (m-30) cc_final: 0.6938 (m-30) REVERT: A 625 GLU cc_start: 0.6884 (pm20) cc_final: 0.6553 (pm20) REVERT: A 752 PHE cc_start: 0.8023 (t80) cc_final: 0.7563 (t80) REVERT: A 776 GLU cc_start: 0.7361 (tp30) cc_final: 0.6868 (tp30) REVERT: A 822 MET cc_start: 0.7653 (ttm) cc_final: 0.7327 (ttm) REVERT: A 856 LYS cc_start: 0.7936 (mttm) cc_final: 0.7722 (mptt) REVERT: A 863 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7171 (ttm-80) REVERT: A 922 LYS cc_start: 0.8269 (tmmt) cc_final: 0.7538 (tttp) REVERT: B 75 LYS cc_start: 0.7705 (mmmt) cc_final: 0.7489 (mttp) REVERT: B 92 MET cc_start: 0.8500 (ttt) cc_final: 0.8166 (ttm) REVERT: B 100 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7529 (t70) REVERT: B 127 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7302 (mpp80) REVERT: B 144 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8089 (mmtt) REVERT: B 155 ASN cc_start: 0.8240 (t0) cc_final: 0.7905 (t0) REVERT: B 156 ASP cc_start: 0.7638 (p0) cc_final: 0.7313 (p0) REVERT: B 222 TYR cc_start: 0.7992 (m-80) cc_final: 0.7711 (m-80) REVERT: B 236 GLU cc_start: 0.6518 (pm20) cc_final: 0.6112 (pm20) REVERT: B 343 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7276 (mmmm) REVERT: B 360 MET cc_start: 0.7809 (mmm) cc_final: 0.7466 (tpp) REVERT: C 21 MET cc_start: 0.8404 (mmm) cc_final: 0.8201 (mmm) REVERT: C 91 MET cc_start: 0.5442 (tpt) cc_final: 0.5055 (tpt) REVERT: C 266 LEU cc_start: 0.7637 (tp) cc_final: 0.7414 (tt) REVERT: C 272 LYS cc_start: 0.7582 (pttt) cc_final: 0.7355 (pttt) REVERT: C 329 MET cc_start: 0.6557 (tpp) cc_final: 0.6188 (mpp) REVERT: D 206 TRP cc_start: 0.8492 (t-100) cc_final: 0.8195 (t-100) outliers start: 38 outliers final: 25 residues processed: 316 average time/residue: 0.1248 time to fit residues: 53.3231 Evaluate side-chains 315 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 124 optimal weight: 0.0050 chunk 99 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.170956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142983 restraints weight = 16198.222| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.58 r_work: 0.3692 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10644 Z= 0.138 Angle : 0.695 14.306 14367 Z= 0.338 Chirality : 0.043 0.227 1534 Planarity : 0.004 0.049 1862 Dihedral : 4.216 23.193 1408 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 29.15 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.51 (0.24), residues: 1260 helix: 1.27 (0.20), residues: 691 sheet: -0.59 (0.61), residues: 74 loop : -0.79 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 279 TYR 0.028 0.002 TYR B 304 PHE 0.030 0.002 PHE A 362 TRP 0.022 0.002 TRP A 428 HIS 0.006 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00317 (10627) covalent geometry : angle 0.67939 (14352) hydrogen bonds : bond 0.03629 ( 523) hydrogen bonds : angle 4.43849 ( 1521) metal coordination : bond 0.01032 ( 17) metal coordination : angle 4.64016 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 SER cc_start: 0.7309 (t) cc_final: 0.6961 (p) REVERT: A 328 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7359 (mm) REVERT: A 444 LYS cc_start: 0.5415 (mttt) cc_final: 0.3928 (ptpt) REVERT: A 457 ASP cc_start: 0.7609 (m-30) cc_final: 0.7075 (m-30) REVERT: A 470 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 493 LYS cc_start: 0.7636 (tptp) cc_final: 0.7372 (tptp) REVERT: A 546 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 570 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7967 (ttmt) REVERT: A 596 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 597 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 601 ASP cc_start: 0.7201 (m-30) cc_final: 0.6922 (m-30) REVERT: A 602 GLU cc_start: 0.7273 (tt0) cc_final: 0.6967 (tt0) REVERT: A 752 PHE cc_start: 0.8048 (t80) cc_final: 0.7840 (t80) REVERT: A 811 GLU cc_start: 0.6286 (mt-10) cc_final: 0.5887 (mt-10) REVERT: A 822 MET cc_start: 0.7638 (ttm) cc_final: 0.7232 (ttm) REVERT: A 842 GLU cc_start: 0.7855 (pp20) cc_final: 0.7601 (tm-30) REVERT: A 856 LYS cc_start: 0.7938 (mttm) cc_final: 0.7736 (mptt) REVERT: A 863 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7173 (ttm-80) REVERT: A 922 LYS cc_start: 0.8302 (tmmt) cc_final: 0.7561 (tttp) REVERT: A 935 THR cc_start: 0.8287 (m) cc_final: 0.7823 (p) REVERT: B 75 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7430 (mttp) REVERT: B 92 MET cc_start: 0.8471 (ttt) cc_final: 0.8120 (ttm) REVERT: B 100 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7496 (t70) REVERT: B 127 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7294 (mpp80) REVERT: B 144 LYS cc_start: 0.8494 (mmtp) cc_final: 0.8082 (mmtt) REVERT: B 155 ASN cc_start: 0.8256 (t0) cc_final: 0.7927 (t0) REVERT: B 156 ASP cc_start: 0.7647 (p0) cc_final: 0.7341 (p0) REVERT: B 236 GLU cc_start: 0.6480 (pm20) cc_final: 0.6157 (pm20) REVERT: B 343 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7113 (mmmm) REVERT: B 360 MET cc_start: 0.7735 (mmm) cc_final: 0.7385 (tpp) REVERT: C 91 MET cc_start: 0.5419 (tpt) cc_final: 0.4980 (tpt) REVERT: C 266 LEU cc_start: 0.7641 (tp) cc_final: 0.7429 (tt) REVERT: C 272 LYS cc_start: 0.7592 (pttt) cc_final: 0.7367 (pttt) REVERT: C 329 MET cc_start: 0.6545 (tpp) cc_final: 0.6131 (mpp) REVERT: D 206 TRP cc_start: 0.8491 (t-100) cc_final: 0.8189 (t-100) REVERT: D 272 LEU cc_start: 0.7450 (mp) cc_final: 0.7159 (mt) outliers start: 34 outliers final: 21 residues processed: 302 average time/residue: 0.1319 time to fit residues: 53.5679 Evaluate side-chains 309 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.0570 chunk 85 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.0060 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 25 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.171094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.143131 restraints weight = 16354.688| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.61 r_work: 0.3696 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10644 Z= 0.137 Angle : 0.693 14.005 14367 Z= 0.339 Chirality : 0.043 0.220 1534 Planarity : 0.004 0.050 1862 Dihedral : 4.225 24.964 1408 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.74 % Allowed : 29.42 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.28 (0.20), residues: 691 sheet: -0.63 (0.62), residues: 74 loop : -0.76 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 35 TYR 0.024 0.001 TYR D 329 PHE 0.028 0.001 PHE A 743 TRP 0.036 0.002 TRP A 428 HIS 0.004 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00315 (10627) covalent geometry : angle 0.67788 (14352) hydrogen bonds : bond 0.03626 ( 523) hydrogen bonds : angle 4.44452 ( 1521) metal coordination : bond 0.00969 ( 17) metal coordination : angle 4.46597 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.39 seconds wall clock time: 47 minutes 53.62 seconds (2873.62 seconds total)