Starting phenix.real_space_refine on Mon Jun 9 05:43:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c60_16449/06_2025/8c60_16449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c60_16449/06_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_16449/06_2025/8c60_16449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c60_16449/06_2025/8c60_16449.map" model { file = "/net/cci-nas-00/data/ceres_data/8c60_16449/06_2025/8c60_16449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c60_16449/06_2025/8c60_16449.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG: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: 6.97, per 1000 atoms: 0.67 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: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.96 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: 2.97 Time building geometry restraints manager: 3.33 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- 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 : 16.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (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 TRP 0.039 0.002 TRP A 560 HIS 0.004 0.001 HIS C 297 PHE 0.031 0.002 PHE A 743 TYR 0.036 0.002 TYR D 236 ARG 0.020 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.13965 ( 523) hydrogen bonds : angle 6.04310 ( 1521) metal coordination : bond 0.01875 ( 17) metal coordination : angle 4.64279 ( 15) covalent geometry : bond 0.00372 (10627) covalent geometry : angle 0.78346 (14352) *********************** 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 : 1.098 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: 0.8063 (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: 0.7604 (mt0) REVERT: A 776 GLU cc_start: 0.7120 (tp30) cc_final: 0.6705 (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: 0.7546 (mpp) REVERT: A 922 LYS cc_start: 0.8008 (tmmt) cc_final: 0.7782 (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: 0.6626 (p0) outliers start: 9 outliers final: 1 residues processed: 281 average time/residue: 0.2672 time to fit residues: 100.7792 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 : 1.184 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 114 optimal weight: 10.0000 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 859 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.179228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.152120 restraints weight = 16442.471| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.75 r_work: 0.3796 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10644 Z= 0.130 Angle : 0.647 15.320 14367 Z= 0.317 Chirality : 0.043 0.294 1534 Planarity : 0.005 0.068 1862 Dihedral : 4.307 24.604 1413 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.27 % Allowed : 24.82 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1260 helix: 1.24 (0.20), residues: 671 sheet: -0.41 (0.63), residues: 74 loop : -0.87 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 560 HIS 0.008 0.001 HIS B 58 PHE 0.026 0.002 PHE A 743 TYR 0.027 0.002 TYR D 329 ARG 0.006 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 523) hydrogen bonds : angle 4.68088 ( 1521) metal coordination : bond 0.00960 ( 17) metal coordination : angle 4.28132 ( 15) covalent geometry : bond 0.00285 (10627) covalent geometry : angle 0.63254 (14352) *********************** 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 316 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7281 (m-30) cc_final: 0.7052 (m-30) REVERT: A 503 THR cc_start: 0.7834 (p) cc_final: 0.7480 (m) REVERT: A 540 LYS cc_start: 0.7633 (mttp) cc_final: 0.7410 (mttp) REVERT: A 545 LYS cc_start: 0.7519 (tptt) cc_final: 0.7011 (tptm) REVERT: A 557 ASN cc_start: 0.7679 (t160) cc_final: 0.7436 (t0) REVERT: A 570 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7705 (ttpp) REVERT: A 741 SER cc_start: 0.8075 (t) cc_final: 0.7516 (p) REVERT: A 787 LEU cc_start: 0.4291 (OUTLIER) cc_final: 0.4042 (tt) REVERT: A 814 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6369 (mt-10) REVERT: A 835 GLN cc_start: 0.7392 (mp10) cc_final: 0.7175 (mp10) REVERT: A 922 LYS cc_start: 0.8077 (tmmt) cc_final: 0.7702 (tptt) REVERT: B 44 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5868 (mp) REVERT: B 75 LYS cc_start: 0.7589 (mmmt) cc_final: 0.7337 (mmmt) REVERT: B 127 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7030 (mpp80) REVERT: B 131 ASP cc_start: 0.6582 (p0) cc_final: 0.6374 (p0) REVERT: B 151 PHE cc_start: 0.8515 (m-10) cc_final: 0.8076 (m-80) REVERT: B 185 GLU cc_start: 0.7347 (tt0) cc_final: 0.7063 (tt0) REVERT: B 243 LYS cc_start: 0.7921 (tttp) cc_final: 0.7681 (ttpt) REVERT: B 336 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7233 (mm-30) REVERT: C 20 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7303 (tt) REVERT: C 298 MET cc_start: 0.8022 (mmm) cc_final: 0.7789 (mmt) REVERT: C 305 LEU cc_start: 0.8146 (mt) cc_final: 0.7866 (mp) outliers start: 37 outliers final: 15 residues processed: 293 average time/residue: 0.3233 time to fit residues: 126.5171 Evaluate side-chains 272 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 842 GLU 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 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 C residue 20 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 272 LYS 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 78 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN A 867 HIS ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.173131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145156 restraints weight = 16176.539| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.73 r_work: 0.3698 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 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 = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10644 Z= 0.166 Angle : 0.651 15.376 14367 Z= 0.316 Chirality : 0.043 0.222 1534 Planarity : 0.004 0.049 1862 Dihedral : 4.165 22.039 1408 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.27 % Allowed : 25.18 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1260 helix: 1.33 (0.20), residues: 675 sheet: -0.41 (0.63), residues: 75 loop : -0.85 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 560 HIS 0.005 0.001 HIS C 297 PHE 0.015 0.002 PHE A 925 TYR 0.024 0.002 TYR D 329 ARG 0.006 0.001 ARG A 588 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 523) hydrogen bonds : angle 4.58452 ( 1521) metal coordination : bond 0.00805 ( 17) metal coordination : angle 4.36134 ( 15) covalent geometry : bond 0.00374 (10627) covalent geometry : angle 0.63562 (14352) *********************** 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 332 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.7469 (m-80) cc_final: 0.7167 (m-10) REVERT: A 444 LYS cc_start: 0.5239 (mttt) cc_final: 0.3808 (ptpt) REVERT: A 457 ASP cc_start: 0.7530 (m-30) cc_final: 0.7156 (m-30) REVERT: A 458 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 470 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 475 VAL cc_start: 0.7909 (t) cc_final: 0.7683 (p) REVERT: A 522 GLU cc_start: 0.7355 (mp0) cc_final: 0.7067 (mp0) REVERT: A 546 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6830 (tm-30) REVERT: A 601 ASP cc_start: 0.6806 (m-30) cc_final: 0.6533 (m-30) REVERT: A 787 LEU cc_start: 0.4453 (OUTLIER) cc_final: 0.4204 (tt) REVERT: A 814 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6575 (mt-10) REVERT: A 822 MET cc_start: 0.7873 (ttm) cc_final: 0.7667 (ttm) REVERT: A 835 GLN cc_start: 0.7501 (mp10) cc_final: 0.7168 (mp10) REVERT: A 857 LEU cc_start: 0.7673 (tp) cc_final: 0.7292 (tt) REVERT: A 922 LYS cc_start: 0.8135 (tmmt) cc_final: 0.7564 (tptm) REVERT: A 936 ILE cc_start: 0.8109 (pt) cc_final: 0.7762 (mt) REVERT: B 75 LYS cc_start: 0.7594 (mmmt) cc_final: 0.7354 (mtmm) REVERT: B 91 GLN cc_start: 0.8227 (mt0) cc_final: 0.8008 (mt0) REVERT: B 127 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7240 (mpp80) REVERT: B 131 ASP cc_start: 0.6824 (p0) cc_final: 0.6598 (p0) REVERT: B 151 PHE cc_start: 0.8576 (m-10) cc_final: 0.8110 (m-80) REVERT: B 155 ASN cc_start: 0.8227 (t0) cc_final: 0.7929 (t0) REVERT: B 185 GLU cc_start: 0.7662 (tt0) cc_final: 0.7450 (tt0) REVERT: B 211 ASP cc_start: 0.7085 (m-30) cc_final: 0.6830 (t0) REVERT: B 336 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 360 MET cc_start: 0.7878 (mmt) cc_final: 0.7411 (mmm) REVERT: C 91 MET cc_start: 0.5353 (tpt) cc_final: 0.5120 (tpt) REVERT: C 286 LEU cc_start: 0.8360 (mt) cc_final: 0.8094 (mm) REVERT: D 206 TRP cc_start: 0.8539 (t-100) cc_final: 0.8333 (t-100) REVERT: D 261 LYS cc_start: 0.8152 (mttm) cc_final: 0.7920 (mttm) REVERT: D 265 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6739 (m110) outliers start: 37 outliers final: 19 residues processed: 313 average time/residue: 0.2823 time to fit residues: 117.6220 Evaluate side-chains 288 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 470 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 593 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 61 THR Chi-restraints excluded: chain B residue 66 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 225 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 343 LYS 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 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 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 773 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140971 restraints weight = 16128.596| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.55 r_work: 0.3644 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 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 = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10644 Z= 0.193 Angle : 0.668 16.909 14367 Z= 0.327 Chirality : 0.044 0.201 1534 Planarity : 0.004 0.048 1862 Dihedral : 4.230 20.870 1408 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.80 % Allowed : 25.35 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1260 helix: 1.25 (0.20), residues: 672 sheet: -0.38 (0.63), residues: 74 loop : -0.96 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 206 HIS 0.006 0.001 HIS C 318 PHE 0.022 0.002 PHE A 362 TYR 0.026 0.002 TYR D 329 ARG 0.005 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 523) hydrogen bonds : angle 4.53745 ( 1521) metal coordination : bond 0.00789 ( 17) metal coordination : angle 4.78728 ( 15) covalent geometry : bond 0.00424 (10627) covalent geometry : angle 0.65046 (14352) *********************** 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 345 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 TRP cc_start: 0.8569 (m100) cc_final: 0.7927 (m100) REVERT: A 457 ASP cc_start: 0.7602 (m-30) cc_final: 0.7085 (m-30) REVERT: A 458 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 470 LEU cc_start: 0.8483 (mp) cc_final: 0.8235 (mm) REVERT: A 475 VAL cc_start: 0.8101 (t) cc_final: 0.7867 (p) REVERT: A 480 GLN cc_start: 0.7493 (tp40) cc_final: 0.7060 (tp-100) REVERT: A 519 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7420 (mtmm) REVERT: A 522 GLU cc_start: 0.7411 (mp0) cc_final: 0.7146 (mp0) REVERT: A 546 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 559 ILE cc_start: 0.7462 (mt) cc_final: 0.7094 (mt) REVERT: A 580 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7718 (mtmm) REVERT: A 597 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 601 ASP cc_start: 0.7033 (m-30) cc_final: 0.6723 (m-30) REVERT: A 602 GLU cc_start: 0.7273 (tt0) cc_final: 0.6818 (tt0) REVERT: A 643 ARG cc_start: 0.6911 (mtt-85) cc_final: 0.6606 (mtt-85) REVERT: A 741 SER cc_start: 0.8231 (t) cc_final: 0.7520 (p) REVERT: A 776 GLU cc_start: 0.7407 (tp30) cc_final: 0.7056 (tp30) REVERT: A 787 LEU cc_start: 0.4480 (OUTLIER) cc_final: 0.4244 (tt) REVERT: A 835 GLN cc_start: 0.7490 (mp10) cc_final: 0.7158 (mp10) REVERT: A 855 ASP cc_start: 0.7372 (p0) cc_final: 0.7064 (p0) REVERT: A 915 MET cc_start: 0.6247 (mpp) cc_final: 0.5687 (mpp) REVERT: A 922 LYS cc_start: 0.8222 (tmmt) cc_final: 0.7601 (tptm) REVERT: A 924 MET cc_start: 0.7114 (ttm) cc_final: 0.6724 (ttm) REVERT: A 925 PHE cc_start: 0.7956 (m-80) cc_final: 0.7463 (m-80) REVERT: A 935 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7739 (t) REVERT: B 44 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6486 (mp) REVERT: B 45 ASN cc_start: 0.7365 (m110) cc_final: 0.7146 (m-40) REVERT: B 49 TYR cc_start: 0.6420 (p90) cc_final: 0.6170 (p90) REVERT: B 74 ILE cc_start: 0.7515 (mm) cc_final: 0.7226 (mm) REVERT: B 75 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7403 (mtmm) REVERT: B 91 GLN cc_start: 0.8202 (mt0) cc_final: 0.7949 (mt0) REVERT: B 92 MET cc_start: 0.8557 (ttt) cc_final: 0.8251 (ttm) REVERT: B 100 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7540 (t0) REVERT: B 127 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7354 (mpp80) REVERT: B 131 ASP cc_start: 0.6966 (p0) cc_final: 0.6715 (p0) REVERT: B 146 SER cc_start: 0.8649 (t) cc_final: 0.8416 (t) REVERT: B 155 ASN cc_start: 0.8284 (t0) cc_final: 0.7920 (t0) REVERT: B 156 ASP cc_start: 0.7751 (p0) cc_final: 0.7401 (p0) REVERT: B 294 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 336 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7064 (tm-30) REVERT: B 360 MET cc_start: 0.7872 (mmt) cc_final: 0.7337 (mmm) REVERT: C 21 MET cc_start: 0.8341 (mmm) cc_final: 0.8036 (mmm) REVERT: C 91 MET cc_start: 0.5353 (tpt) cc_final: 0.5055 (tpt) REVERT: C 286 LEU cc_start: 0.8423 (mt) cc_final: 0.8208 (mm) REVERT: C 295 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7733 (mt) REVERT: C 329 MET cc_start: 0.6645 (tpp) cc_final: 0.6249 (mpp) REVERT: D 206 TRP cc_start: 0.8600 (t-100) cc_final: 0.8361 (t-100) REVERT: D 293 MET cc_start: 0.2523 (OUTLIER) cc_final: 0.2291 (mmp) outliers start: 43 outliers final: 21 residues processed: 323 average time/residue: 0.2675 time to fit residues: 116.9904 Evaluate side-chains 328 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 490 ASP Chi-restraints excluded: chain A residue 519 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 607 HIS Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 659 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 107 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 293 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** 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 660 HIS ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141544 restraints weight = 16082.246| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.63 r_work: 0.3667 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10644 Z= 0.142 Angle : 0.634 16.459 14367 Z= 0.307 Chirality : 0.043 0.339 1534 Planarity : 0.004 0.048 1862 Dihedral : 4.148 22.715 1408 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.09 % Allowed : 28.09 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1260 helix: 1.44 (0.20), residues: 667 sheet: -0.26 (0.63), residues: 75 loop : -0.96 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 560 HIS 0.014 0.001 HIS A 847 PHE 0.020 0.001 PHE A 752 TYR 0.025 0.001 TYR D 329 ARG 0.006 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 523) hydrogen bonds : angle 4.45630 ( 1521) metal coordination : bond 0.01067 ( 17) metal coordination : angle 4.51893 ( 15) covalent geometry : bond 0.00322 (10627) covalent geometry : angle 0.61724 (14352) *********************** 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: 35 poor density : 306 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7673 (m-30) cc_final: 0.7085 (m-30) REVERT: A 458 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 470 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8261 (mm) REVERT: A 475 VAL cc_start: 0.8154 (t) cc_final: 0.7842 (p) REVERT: A 480 GLN cc_start: 0.7512 (tp40) cc_final: 0.7096 (tp-100) REVERT: A 505 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 519 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7381 (mtmm) REVERT: A 522 GLU cc_start: 0.7391 (mp0) cc_final: 0.7129 (mp0) REVERT: A 559 ILE cc_start: 0.7551 (mt) cc_final: 0.7156 (mt) REVERT: A 580 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7758 (mtmm) REVERT: A 597 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 601 ASP cc_start: 0.7053 (m-30) cc_final: 0.6730 (m-30) REVERT: A 602 GLU cc_start: 0.7197 (tt0) cc_final: 0.6872 (tt0) REVERT: A 625 GLU cc_start: 0.6915 (pm20) cc_final: 0.6054 (pm20) REVERT: A 643 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6563 (mtt-85) REVERT: A 741 SER cc_start: 0.8208 (t) cc_final: 0.7556 (p) REVERT: A 743 PHE cc_start: 0.8236 (t80) cc_final: 0.8020 (t80) REVERT: A 752 PHE cc_start: 0.7903 (t80) cc_final: 0.7488 (t80) REVERT: A 776 GLU cc_start: 0.7293 (tp30) cc_final: 0.6905 (tp30) REVERT: A 787 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.4210 (tt) REVERT: A 835 GLN cc_start: 0.7434 (mp10) cc_final: 0.7103 (mp10) REVERT: A 854 MET cc_start: 0.8427 (mmm) cc_final: 0.8139 (mmt) REVERT: A 855 ASP cc_start: 0.7396 (p0) cc_final: 0.6970 (p0) REVERT: A 856 LYS cc_start: 0.7892 (mttm) cc_final: 0.7489 (mptt) REVERT: A 915 MET cc_start: 0.6423 (mpp) cc_final: 0.6015 (ttt) REVERT: A 922 LYS cc_start: 0.8260 (tmmt) cc_final: 0.7575 (tptm) REVERT: A 924 MET cc_start: 0.7123 (ttm) cc_final: 0.6769 (ttm) REVERT: A 925 PHE cc_start: 0.8100 (m-80) cc_final: 0.7752 (m-80) REVERT: A 935 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7634 (t) REVERT: B 45 ASN cc_start: 0.7330 (m110) cc_final: 0.7125 (m-40) REVERT: B 49 TYR cc_start: 0.6329 (p90) cc_final: 0.6106 (p90) REVERT: B 74 ILE cc_start: 0.7532 (mm) cc_final: 0.7204 (mm) REVERT: B 75 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7377 (mtmm) REVERT: B 91 GLN cc_start: 0.8251 (mt0) cc_final: 0.7991 (mt0) REVERT: B 92 MET cc_start: 0.8515 (ttt) cc_final: 0.8133 (ttm) REVERT: B 100 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7416 (t0) REVERT: B 112 GLN cc_start: 0.8314 (mt0) cc_final: 0.8087 (mt0) REVERT: B 127 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7280 (mpp80) REVERT: B 131 ASP cc_start: 0.6851 (p0) cc_final: 0.6640 (p0) REVERT: B 144 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8283 (mmtp) REVERT: B 146 SER cc_start: 0.8625 (t) cc_final: 0.8388 (t) REVERT: B 155 ASN cc_start: 0.8260 (t0) cc_final: 0.7885 (t0) REVERT: B 156 ASP cc_start: 0.7648 (p0) cc_final: 0.7331 (p0) REVERT: B 294 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 336 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7057 (tm-30) REVERT: B 360 MET cc_start: 0.7831 (mmt) cc_final: 0.7302 (mmm) REVERT: C 21 MET cc_start: 0.8273 (mmm) cc_final: 0.8007 (mmm) REVERT: C 91 MET cc_start: 0.5414 (tpt) cc_final: 0.5039 (tpt) REVERT: C 295 LEU cc_start: 0.8112 (mm) cc_final: 0.7705 (mt) REVERT: C 329 MET cc_start: 0.6514 (tpp) cc_final: 0.6150 (mpp) REVERT: D 206 TRP cc_start: 0.8583 (t-100) cc_final: 0.8355 (t-100) outliers start: 35 outliers final: 18 residues processed: 323 average time/residue: 0.2608 time to fit residues: 113.3645 Evaluate side-chains 324 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 299 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 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 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 837 GLU Chi-restraints excluded: chain A residue 935 THR 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 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 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 11 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 771 GLN A 773 GLN B 142 HIS B 261 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4174 r_free = 0.4174 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141425 restraints weight = 16124.511| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.58 r_work: 0.3673 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10644 Z= 0.141 Angle : 0.638 16.541 14367 Z= 0.309 Chirality : 0.043 0.322 1534 Planarity : 0.004 0.047 1862 Dihedral : 4.177 22.961 1408 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.62 % Allowed : 27.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1260 helix: 1.49 (0.20), residues: 666 sheet: -0.23 (0.63), residues: 75 loop : -0.86 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 560 HIS 0.003 0.001 HIS C 297 PHE 0.026 0.002 PHE B 188 TYR 0.029 0.002 TYR B 16 ARG 0.006 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 523) hydrogen bonds : angle 4.40686 ( 1521) metal coordination : bond 0.00845 ( 17) metal coordination : angle 4.57657 ( 15) covalent geometry : bond 0.00319 (10627) covalent geometry : angle 0.62141 (14352) *********************** 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 345 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.7630 (t80) cc_final: 0.7114 (t80) REVERT: A 401 TYR cc_start: 0.7508 (m-10) cc_final: 0.7050 (m-10) REVERT: A 457 ASP cc_start: 0.7624 (m-30) cc_final: 0.7062 (m-30) REVERT: A 458 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7194 (mt-10) REVERT: A 470 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8284 (mm) REVERT: A 475 VAL cc_start: 0.8312 (t) cc_final: 0.7968 (p) REVERT: A 480 GLN cc_start: 0.7562 (tp40) cc_final: 0.7160 (tp-100) REVERT: A 505 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 519 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7544 (mtmm) REVERT: A 522 GLU cc_start: 0.7347 (mp0) cc_final: 0.7141 (mp0) REVERT: A 597 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 601 ASP cc_start: 0.7154 (m-30) cc_final: 0.6859 (m-30) REVERT: A 625 GLU cc_start: 0.6928 (pm20) cc_final: 0.6623 (pm20) REVERT: A 643 ARG cc_start: 0.6979 (mtt-85) cc_final: 0.6551 (mtt-85) REVERT: A 741 SER cc_start: 0.8216 (t) cc_final: 0.7551 (p) REVERT: A 743 PHE cc_start: 0.8187 (t80) cc_final: 0.7974 (t80) REVERT: A 746 ASN cc_start: 0.8326 (p0) cc_final: 0.8094 (p0) REVERT: A 752 PHE cc_start: 0.7952 (t80) cc_final: 0.7529 (t80) REVERT: A 776 GLU cc_start: 0.7292 (tp30) cc_final: 0.6900 (tp30) REVERT: A 835 GLN cc_start: 0.7361 (mp10) cc_final: 0.7119 (mp10) REVERT: A 854 MET cc_start: 0.8437 (mmm) cc_final: 0.7888 (mmt) REVERT: A 855 ASP cc_start: 0.7479 (p0) cc_final: 0.7172 (p0) REVERT: A 856 LYS cc_start: 0.7954 (mttm) cc_final: 0.7573 (mptt) REVERT: A 863 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6993 (ttm-80) REVERT: A 915 MET cc_start: 0.6429 (mpp) cc_final: 0.6035 (ttt) REVERT: A 922 LYS cc_start: 0.8173 (tmmt) cc_final: 0.7530 (tttp) REVERT: A 924 MET cc_start: 0.7011 (ttm) cc_final: 0.6523 (ttm) REVERT: A 935 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7468 (p) REVERT: B 74 ILE cc_start: 0.7546 (mm) cc_final: 0.7241 (mm) REVERT: B 75 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7436 (mttp) REVERT: B 91 GLN cc_start: 0.8207 (mt0) cc_final: 0.7992 (mt0) REVERT: B 92 MET cc_start: 0.8534 (ttt) cc_final: 0.8175 (ttm) REVERT: B 127 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7237 (mpp80) REVERT: B 129 GLN cc_start: 0.7581 (mt0) cc_final: 0.7327 (mt0) REVERT: B 131 ASP cc_start: 0.6782 (p0) cc_final: 0.6577 (p0) REVERT: B 144 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8132 (mmtt) REVERT: B 146 SER cc_start: 0.8714 (t) cc_final: 0.8494 (t) REVERT: B 155 ASN cc_start: 0.8255 (t0) cc_final: 0.7927 (t0) REVERT: B 222 TYR cc_start: 0.8062 (m-80) cc_final: 0.7842 (m-80) REVERT: B 336 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6979 (mm-30) REVERT: B 360 MET cc_start: 0.7830 (mmt) cc_final: 0.7370 (mmm) REVERT: C 21 MET cc_start: 0.8285 (mmm) cc_final: 0.7939 (mmm) REVERT: C 91 MET cc_start: 0.5422 (tpt) cc_final: 0.5045 (tpt) REVERT: C 287 ILE cc_start: 0.8550 (mp) cc_final: 0.8297 (mp) REVERT: C 295 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7789 (mt) REVERT: C 329 MET cc_start: 0.6572 (tpp) cc_final: 0.6192 (mpp) REVERT: D 206 TRP cc_start: 0.8577 (t-100) cc_final: 0.8345 (t-100) outliers start: 41 outliers final: 23 residues processed: 323 average time/residue: 0.2784 time to fit residues: 122.3660 Evaluate side-chains 325 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 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 470 LEU 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 607 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 112 GLN B 240 GLN A ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** 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 = 0.4175 r_free = 0.4175 target = 0.170472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141817 restraints weight = 16275.575| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.59 r_work: 0.3673 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.136 Angle : 0.655 15.639 14367 Z= 0.319 Chirality : 0.044 0.413 1534 Planarity : 0.004 0.046 1862 Dihedral : 4.180 23.585 1408 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.45 % Allowed : 28.53 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1260 helix: 1.48 (0.20), residues: 668 sheet: -0.25 (0.62), residues: 75 loop : -0.74 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 313 HIS 0.004 0.001 HIS C 297 PHE 0.028 0.001 PHE B 188 TYR 0.034 0.001 TYR B 16 ARG 0.005 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 523) hydrogen bonds : angle 4.40000 ( 1521) metal coordination : bond 0.00980 ( 17) metal coordination : angle 4.39101 ( 15) covalent geometry : bond 0.00308 (10627) covalent geometry : angle 0.63968 (14352) *********************** 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 337 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.7666 (t80) cc_final: 0.7148 (t80) REVERT: A 401 TYR cc_start: 0.7331 (m-10) cc_final: 0.7051 (m-10) REVERT: A 402 ARG cc_start: 0.7313 (ptp90) cc_final: 0.7112 (ptp90) REVERT: A 457 ASP cc_start: 0.7625 (m-30) cc_final: 0.7105 (m-30) REVERT: A 458 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 470 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 475 VAL cc_start: 0.8446 (t) cc_final: 0.8101 (p) REVERT: A 480 GLN cc_start: 0.7585 (tp40) cc_final: 0.7181 (tp-100) REVERT: A 492 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.5118 (pm20) REVERT: A 493 LYS cc_start: 0.7545 (tptp) cc_final: 0.7328 (tptp) REVERT: A 505 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 519 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7578 (mtmm) REVERT: A 522 GLU cc_start: 0.7476 (mp0) cc_final: 0.7229 (mp0) REVERT: A 546 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 597 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 601 ASP cc_start: 0.7240 (m-30) cc_final: 0.6924 (m-30) REVERT: A 625 GLU cc_start: 0.6982 (pm20) cc_final: 0.6695 (pm20) REVERT: A 643 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.6636 (mtt-85) REVERT: A 746 ASN cc_start: 0.8273 (p0) cc_final: 0.8062 (p0) REVERT: A 752 PHE cc_start: 0.7962 (t80) cc_final: 0.7538 (t80) REVERT: A 776 GLU cc_start: 0.7251 (tp30) cc_final: 0.6884 (tp30) REVERT: A 854 MET cc_start: 0.8493 (mmm) cc_final: 0.8257 (mmt) REVERT: A 855 ASP cc_start: 0.7513 (p0) cc_final: 0.7165 (p0) REVERT: A 856 LYS cc_start: 0.7989 (mttm) cc_final: 0.7640 (mptt) REVERT: A 863 ARG cc_start: 0.7341 (ttp-110) cc_final: 0.7046 (ttm-80) REVERT: A 915 MET cc_start: 0.6553 (mpp) cc_final: 0.6095 (ttt) REVERT: A 922 LYS cc_start: 0.8172 (tmmt) cc_final: 0.7539 (tptm) REVERT: B 31 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7604 (tpt) REVERT: B 32 LYS cc_start: 0.8504 (mttp) cc_final: 0.8271 (mttm) REVERT: B 74 ILE cc_start: 0.7562 (mm) cc_final: 0.7247 (mm) REVERT: B 75 LYS cc_start: 0.7685 (mmmt) cc_final: 0.7456 (mttp) REVERT: B 91 GLN cc_start: 0.8204 (mt0) cc_final: 0.7979 (mt0) REVERT: B 92 MET cc_start: 0.8550 (ttt) cc_final: 0.8197 (ttm) REVERT: B 100 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7521 (t70) REVERT: B 127 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7307 (mpp80) REVERT: B 131 ASP cc_start: 0.6809 (p0) cc_final: 0.6601 (p0) REVERT: B 144 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8289 (mmtp) REVERT: B 146 SER cc_start: 0.8733 (t) cc_final: 0.8502 (t) REVERT: B 155 ASN cc_start: 0.8127 (t0) cc_final: 0.7859 (t0) REVERT: B 185 GLU cc_start: 0.7615 (tt0) cc_final: 0.7321 (tt0) REVERT: B 222 TYR cc_start: 0.7993 (m-80) cc_final: 0.7629 (m-80) REVERT: B 336 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 360 MET cc_start: 0.7789 (mmt) cc_final: 0.7297 (mmm) REVERT: C 21 MET cc_start: 0.8215 (mmm) cc_final: 0.7984 (mmm) REVERT: C 91 MET cc_start: 0.5467 (tpt) cc_final: 0.5129 (tpt) REVERT: C 287 ILE cc_start: 0.8577 (mp) cc_final: 0.8312 (mp) REVERT: C 295 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7751 (mt) REVERT: C 329 MET cc_start: 0.6657 (tpp) cc_final: 0.6254 (mpp) REVERT: D 206 TRP cc_start: 0.8576 (t-100) cc_final: 0.8332 (t-100) outliers start: 39 outliers final: 24 residues processed: 318 average time/residue: 0.3053 time to fit residues: 132.5814 Evaluate side-chains 319 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL 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 348 VAL 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 562 GLU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 607 HIS 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 31 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU 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 225 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 112 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 112 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.170326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141875 restraints weight = 16133.839| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.57 r_work: 0.3673 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10644 Z= 0.141 Angle : 0.667 14.638 14367 Z= 0.325 Chirality : 0.045 0.383 1534 Planarity : 0.005 0.119 1862 Dihedral : 4.204 24.471 1408 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.71 % Allowed : 28.09 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1260 helix: 1.45 (0.20), residues: 677 sheet: -0.24 (0.63), residues: 75 loop : -0.74 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 313 HIS 0.003 0.001 HIS C 297 PHE 0.032 0.002 PHE A 743 TYR 0.039 0.002 TYR B 16 ARG 0.006 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 523) hydrogen bonds : angle 4.40292 ( 1521) metal coordination : bond 0.00820 ( 17) metal coordination : angle 4.24654 ( 15) covalent geometry : bond 0.00320 (10627) covalent geometry : angle 0.65357 (14352) *********************** 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 339 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.7673 (t80) cc_final: 0.7162 (t80) REVERT: A 401 TYR cc_start: 0.7333 (m-10) cc_final: 0.6976 (m-10) REVERT: A 402 ARG cc_start: 0.7308 (ptp90) cc_final: 0.7083 (ptp90) REVERT: A 457 ASP cc_start: 0.7647 (m-30) cc_final: 0.7117 (m-30) REVERT: A 458 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7224 (mt-10) REVERT: A 470 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 475 VAL cc_start: 0.8382 (t) cc_final: 0.8050 (p) REVERT: A 480 GLN cc_start: 0.7604 (tp40) cc_final: 0.7183 (tp-100) REVERT: A 492 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.5157 (pm20) REVERT: A 493 LYS cc_start: 0.7562 (tptp) cc_final: 0.7312 (tptp) REVERT: A 505 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 519 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7610 (mtmm) REVERT: A 522 GLU cc_start: 0.7448 (mp0) cc_final: 0.7200 (mp0) REVERT: A 546 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7143 (tm-30) REVERT: A 597 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 601 ASP cc_start: 0.7279 (m-30) cc_final: 0.6988 (m-30) REVERT: A 625 GLU cc_start: 0.6953 (pm20) cc_final: 0.6669 (pm20) REVERT: A 643 ARG cc_start: 0.7130 (mtt-85) cc_final: 0.6838 (mtt90) REVERT: A 746 ASN cc_start: 0.8211 (p0) cc_final: 0.7989 (p0) REVERT: A 776 GLU cc_start: 0.7349 (tp30) cc_final: 0.6894 (tp30) REVERT: A 854 MET cc_start: 0.8544 (mmm) cc_final: 0.8295 (mmt) REVERT: A 855 ASP cc_start: 0.7552 (p0) cc_final: 0.7195 (p0) REVERT: A 856 LYS cc_start: 0.7957 (mttm) cc_final: 0.7610 (mptt) REVERT: A 863 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.7074 (ttm-80) REVERT: A 915 MET cc_start: 0.6472 (mpp) cc_final: 0.5856 (ttt) REVERT: A 922 LYS cc_start: 0.8135 (tmmt) cc_final: 0.7525 (tptm) REVERT: A 935 THR cc_start: 0.8171 (m) cc_final: 0.7544 (p) REVERT: B 40 HIS cc_start: 0.7597 (t-90) cc_final: 0.7156 (t70) REVERT: B 75 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7459 (mttp) REVERT: B 91 GLN cc_start: 0.8200 (mt0) cc_final: 0.7989 (mt0) REVERT: B 92 MET cc_start: 0.8530 (ttt) cc_final: 0.8189 (ttm) REVERT: B 100 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7585 (t70) REVERT: B 127 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7304 (mpp80) REVERT: B 146 SER cc_start: 0.8751 (t) cc_final: 0.8527 (t) REVERT: B 155 ASN cc_start: 0.8154 (t0) cc_final: 0.7935 (t0) REVERT: B 185 GLU cc_start: 0.7662 (tt0) cc_final: 0.7246 (tt0) REVERT: B 211 ASP cc_start: 0.7273 (t0) cc_final: 0.6977 (m-30) REVERT: B 231 ASP cc_start: 0.8006 (m-30) cc_final: 0.7664 (m-30) REVERT: B 265 ASP cc_start: 0.7845 (p0) cc_final: 0.7588 (p0) REVERT: B 336 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 360 MET cc_start: 0.7827 (mmt) cc_final: 0.7294 (mmm) REVERT: C 21 MET cc_start: 0.8259 (mmm) cc_final: 0.7990 (mmm) REVERT: C 91 MET cc_start: 0.5514 (tpt) cc_final: 0.5049 (tpt) REVERT: C 295 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7764 (mt) REVERT: C 329 MET cc_start: 0.6690 (tpp) cc_final: 0.6244 (mpp) REVERT: D 206 TRP cc_start: 0.8569 (t-100) cc_final: 0.8329 (t-100) outliers start: 42 outliers final: 28 residues processed: 318 average time/residue: 0.2653 time to fit residues: 114.2793 Evaluate side-chains 320 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL 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 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 519 LYS 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 607 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 303 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 657 GLN A 771 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140469 restraints weight = 16218.860| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.61 r_work: 0.3657 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 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 = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10644 Z= 0.159 Angle : 0.694 14.823 14367 Z= 0.337 Chirality : 0.045 0.373 1534 Planarity : 0.004 0.065 1862 Dihedral : 4.235 23.887 1408 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.27 % Allowed : 28.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1260 helix: 1.24 (0.20), residues: 693 sheet: -0.09 (0.63), residues: 74 loop : -0.83 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 428 HIS 0.004 0.001 HIS A 847 PHE 0.026 0.002 PHE A 743 TYR 0.039 0.002 TYR B 16 ARG 0.007 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 523) hydrogen bonds : angle 4.43849 ( 1521) metal coordination : bond 0.00783 ( 17) metal coordination : angle 4.60497 ( 15) covalent geometry : bond 0.00362 (10627) covalent geometry : angle 0.67805 (14352) *********************** 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 327 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.7658 (t80) cc_final: 0.7152 (t80) REVERT: A 402 ARG cc_start: 0.7324 (ptp90) cc_final: 0.6782 (ptp90) REVERT: A 431 PHE cc_start: 0.8012 (m-10) cc_final: 0.7721 (m-80) REVERT: A 457 ASP cc_start: 0.7644 (m-30) cc_final: 0.7114 (m-30) REVERT: A 458 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 470 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 475 VAL cc_start: 0.8387 (t) cc_final: 0.8053 (p) REVERT: A 480 GLN cc_start: 0.7614 (tp40) cc_final: 0.7179 (tp-100) REVERT: A 483 LEU cc_start: 0.7895 (mp) cc_final: 0.7581 (tp) REVERT: A 492 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5307 (pm20) REVERT: A 493 LYS cc_start: 0.7621 (tptp) cc_final: 0.7354 (tptp) REVERT: A 505 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 519 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7735 (mtmm) REVERT: A 522 GLU cc_start: 0.7447 (mp0) cc_final: 0.7230 (mp0) REVERT: A 546 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 597 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 601 ASP cc_start: 0.7368 (m-30) cc_final: 0.7039 (m-30) REVERT: A 625 GLU cc_start: 0.6944 (pm20) cc_final: 0.6672 (pm20) REVERT: A 643 ARG cc_start: 0.7259 (mtt-85) cc_final: 0.6952 (mtt90) REVERT: A 667 PHE cc_start: 0.6252 (m-80) cc_final: 0.5973 (m-80) REVERT: A 746 ASN cc_start: 0.8172 (p0) cc_final: 0.7926 (p0) REVERT: A 828 GLU cc_start: 0.7836 (pt0) cc_final: 0.7591 (pt0) REVERT: A 842 GLU cc_start: 0.7886 (pp20) cc_final: 0.7569 (tm-30) REVERT: A 854 MET cc_start: 0.8559 (mmm) cc_final: 0.8283 (mmt) REVERT: A 855 ASP cc_start: 0.7623 (p0) cc_final: 0.7260 (p0) REVERT: A 856 LYS cc_start: 0.8006 (mttm) cc_final: 0.7661 (mptt) REVERT: A 863 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7159 (ttm-80) REVERT: A 915 MET cc_start: 0.6499 (mpp) cc_final: 0.5856 (ttt) REVERT: A 922 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7534 (tttp) REVERT: B 64 GLU cc_start: 0.8196 (tt0) cc_final: 0.7939 (tp30) REVERT: B 74 ILE cc_start: 0.7632 (mm) cc_final: 0.7328 (mm) REVERT: B 75 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7546 (mttp) REVERT: B 91 GLN cc_start: 0.8234 (mt0) cc_final: 0.7996 (mt0) REVERT: B 92 MET cc_start: 0.8543 (ttt) cc_final: 0.8200 (ttm) REVERT: B 100 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7613 (t70) REVERT: B 127 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7290 (mpp80) REVERT: B 129 GLN cc_start: 0.7638 (mt0) cc_final: 0.7413 (mt0) REVERT: B 146 SER cc_start: 0.8794 (t) cc_final: 0.8568 (t) REVERT: B 155 ASN cc_start: 0.8221 (t0) cc_final: 0.7991 (t0) REVERT: B 231 ASP cc_start: 0.8035 (m-30) cc_final: 0.7681 (m-30) REVERT: B 360 MET cc_start: 0.7875 (mmt) cc_final: 0.7364 (mmm) REVERT: B 373 MET cc_start: 0.7354 (ptp) cc_final: 0.6990 (mtm) REVERT: C 21 MET cc_start: 0.8249 (mmm) cc_final: 0.7902 (mmm) REVERT: C 91 MET cc_start: 0.5471 (tpt) cc_final: 0.5049 (tpt) REVERT: C 295 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7808 (mt) REVERT: C 329 MET cc_start: 0.6700 (tpp) cc_final: 0.6274 (mpp) REVERT: D 206 TRP cc_start: 0.8581 (t-100) cc_final: 0.8342 (t-100) outliers start: 37 outliers final: 26 residues processed: 310 average time/residue: 0.2931 time to fit residues: 123.2241 Evaluate side-chains 317 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 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 479 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 519 LYS 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 607 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain B residue 36 ILE 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 107 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 121 optimal weight: 0.0030 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 261 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.170825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142536 restraints weight = 16169.162| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.61 r_work: 0.3684 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10644 Z= 0.130 Angle : 0.689 13.917 14367 Z= 0.335 Chirality : 0.044 0.386 1534 Planarity : 0.004 0.048 1862 Dihedral : 4.191 26.145 1408 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.39 % Allowed : 29.86 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1260 helix: 1.37 (0.20), residues: 686 sheet: -0.16 (0.64), residues: 75 loop : -0.84 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 428 HIS 0.006 0.001 HIS A 847 PHE 0.029 0.002 PHE A 362 TYR 0.036 0.002 TYR B 16 ARG 0.011 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 523) hydrogen bonds : angle 4.45565 ( 1521) metal coordination : bond 0.01151 ( 17) metal coordination : angle 4.37522 ( 15) covalent geometry : bond 0.00294 (10627) covalent geometry : angle 0.67510 (14352) ********************** 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 314 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.7646 (t80) cc_final: 0.7095 (t80) REVERT: A 402 ARG cc_start: 0.7298 (ptp90) cc_final: 0.6993 (ptp90) REVERT: A 456 GLU cc_start: 0.7674 (tp30) cc_final: 0.7326 (tp30) REVERT: A 457 ASP cc_start: 0.7655 (m-30) cc_final: 0.7074 (m-30) REVERT: A 461 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 470 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 475 VAL cc_start: 0.8355 (t) cc_final: 0.8007 (p) REVERT: A 480 GLN cc_start: 0.7592 (tp40) cc_final: 0.6993 (tp-100) REVERT: A 483 LEU cc_start: 0.7834 (mp) cc_final: 0.7597 (tp) REVERT: A 492 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5335 (pm20) REVERT: A 493 LYS cc_start: 0.7633 (tptp) cc_final: 0.7364 (tptp) REVERT: A 505 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7595 (mt-10) REVERT: A 519 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7703 (mtmm) REVERT: A 522 GLU cc_start: 0.7438 (mp0) cc_final: 0.7213 (mp0) REVERT: A 597 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 601 ASP cc_start: 0.7338 (m-30) cc_final: 0.7019 (m-30) REVERT: A 625 GLU cc_start: 0.6827 (pm20) cc_final: 0.5751 (mt-10) REVERT: A 643 ARG cc_start: 0.7134 (mtt-85) cc_final: 0.6632 (mtt90) REVERT: A 746 ASN cc_start: 0.8121 (p0) cc_final: 0.7900 (p0) REVERT: A 776 GLU cc_start: 0.7240 (tp30) cc_final: 0.6917 (tp30) REVERT: A 842 GLU cc_start: 0.7902 (pp20) cc_final: 0.7580 (tm-30) REVERT: A 855 ASP cc_start: 0.7753 (p0) cc_final: 0.7357 (p0) REVERT: A 856 LYS cc_start: 0.8012 (mttm) cc_final: 0.7685 (mptt) REVERT: A 863 ARG cc_start: 0.7465 (ttp-110) cc_final: 0.7194 (ttm-80) REVERT: A 915 MET cc_start: 0.6456 (mpp) cc_final: 0.5882 (ttt) REVERT: A 922 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7587 (tptt) REVERT: A 928 ARG cc_start: 0.6798 (ptm160) cc_final: 0.6552 (ptm160) REVERT: A 935 THR cc_start: 0.8210 (m) cc_final: 0.7605 (p) REVERT: B 75 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7500 (mttp) REVERT: B 91 GLN cc_start: 0.8212 (mt0) cc_final: 0.7971 (mt0) REVERT: B 92 MET cc_start: 0.8518 (ttt) cc_final: 0.8213 (ttm) REVERT: B 127 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7292 (mpp80) REVERT: B 155 ASN cc_start: 0.8157 (t0) cc_final: 0.7871 (t0) REVERT: B 185 GLU cc_start: 0.7688 (tt0) cc_final: 0.7028 (tt0) REVERT: B 231 ASP cc_start: 0.7977 (m-30) cc_final: 0.7614 (m-30) REVERT: B 360 MET cc_start: 0.7827 (mmt) cc_final: 0.7287 (mmm) REVERT: B 373 MET cc_start: 0.7253 (ptp) cc_final: 0.6897 (mtm) REVERT: C 21 MET cc_start: 0.8168 (mmm) cc_final: 0.7912 (mmm) REVERT: C 91 MET cc_start: 0.5530 (tpt) cc_final: 0.5096 (tpt) REVERT: C 295 LEU cc_start: 0.8072 (mm) cc_final: 0.7758 (mt) REVERT: C 329 MET cc_start: 0.6641 (tpp) cc_final: 0.6208 (mpp) REVERT: D 206 TRP cc_start: 0.8551 (t-100) cc_final: 0.8285 (t-100) outliers start: 27 outliers final: 20 residues processed: 302 average time/residue: 0.2751 time to fit residues: 113.4376 Evaluate side-chains 309 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 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 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 519 LYS 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 742 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 213 LEU 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 D residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 771 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 261 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.170288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142220 restraints weight = 16167.243| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.56 r_work: 0.3681 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4292 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= 0.140 Angle : 0.693 13.808 14367 Z= 0.335 Chirality : 0.045 0.387 1534 Planarity : 0.004 0.072 1862 Dihedral : 4.173 22.618 1408 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.09 % Allowed : 29.86 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1260 helix: 1.37 (0.20), residues: 686 sheet: -0.11 (0.63), residues: 74 loop : -0.78 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 428 HIS 0.007 0.001 HIS B 40 PHE 0.026 0.002 PHE A 743 TYR 0.032 0.001 TYR B 16 ARG 0.007 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 523) hydrogen bonds : angle 4.46083 ( 1521) metal coordination : bond 0.00786 ( 17) metal coordination : angle 4.03611 ( 15) covalent geometry : bond 0.00320 (10627) covalent geometry : angle 0.68054 (14352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6229.98 seconds wall clock time: 109 minutes 51.12 seconds (6591.12 seconds total)