Starting phenix.real_space_refine on Fri Sep 19 11:48:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh3_53153/09_2025/9qh3_53153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh3_53153/09_2025/9qh3_53153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qh3_53153/09_2025/9qh3_53153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh3_53153/09_2025/9qh3_53153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qh3_53153/09_2025/9qh3_53153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh3_53153/09_2025/9qh3_53153.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 8011 2.51 5 N 2243 2.21 5 O 2509 1.98 5 H 12816 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25636 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8378 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 27, 'TRANS': 525} Chain: "B" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8378 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 27, 'TRANS': 525} Chain: "C" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 8378 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 27, 'TRANS': 525} Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 410 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 4.73, per 1000 atoms: 0.18 Number of scatterers: 25636 At special positions: 0 Unit cell: (94.17, 107.31, 127.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 2509 8.00 N 2243 7.00 C 8011 6.00 H 12816 1.00 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: 2.33 Conformation dependent library (CDL) restraints added in 782.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3054 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 39.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 84 through 99 Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.606A pdb=" N ALA A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.622A pdb=" N GLN A 171 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 172 " --> pdb=" O GLN A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 172' Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.588A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 239 through 250 removed outlier: 4.166A pdb=" N ALA A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 262 through 281 Processing helix chain 'A' and resid 291 through 313 removed outlier: 3.593A pdb=" N LYS A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.687A pdb=" N ALA A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 398 through 413 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 438 through 455 removed outlier: 3.710A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.989A pdb=" N HIS A 488 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 540 removed outlier: 3.597A pdb=" N GLN A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 84 through 99 Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 125 through 141 removed outlier: 4.054A pdb=" N GLY B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.801A pdb=" N SER B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.615A pdb=" N SER B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 281 removed outlier: 3.505A pdb=" N PHE B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.552A pdb=" N ALA B 363 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 398 through 413 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 438 through 455 removed outlier: 3.656A pdb=" N ALA B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 539 Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 84 through 99 Proline residue: C 97 - end of helix Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 125 through 141 removed outlier: 4.025A pdb=" N GLY C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.790A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 239 through 258 removed outlier: 5.679A pdb=" N GLU C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 Processing helix chain 'C' and resid 292 through 312 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 398 through 414 removed outlier: 4.607A pdb=" N ALA C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 removed outlier: 3.553A pdb=" N ALA C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 removed outlier: 4.358A pdb=" N LEU C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 539 removed outlier: 3.656A pdb=" N LEU C 524 " --> pdb=" O MET C 520 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 529 " --> pdb=" O GLY C 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1007 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.382A pdb=" N SER A 38 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER A 59 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS A 114 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS A 61 " --> pdb=" O CYS A 114 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL A 116 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLN A 63 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N SER A 118 " --> pdb=" O GLN A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.086A pdb=" N PHE A 155 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 175 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 190 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N ASP A 509 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N GLU A 192 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N GLN A 507 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP A 194 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ALA A 505 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 497 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 506 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 495 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N MET A 508 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP A 493 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 475 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 332 removed outlier: 6.088A pdb=" N GLN A 350 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 368 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 10 removed outlier: 6.477A pdb=" N SER B 38 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.948A pdb=" N PHE B 155 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 175 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 176 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER B 191 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 189 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 180 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N GLU B 192 " --> pdb=" O GLN B 507 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLN B 507 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ASP B 194 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ALA B 505 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 328 through 332 removed outlier: 6.019A pdb=" N GLN B 350 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 10 removed outlier: 3.594A pdb=" N SER C 13 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER C 38 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163 removed outlier: 10.471A pdb=" N GLU C 190 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N ASP C 509 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLU C 192 " --> pdb=" O GLN C 507 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N GLN C 507 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N ASP C 194 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ALA C 505 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 497 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 506 " --> pdb=" O LYS C 495 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS C 495 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET C 508 " --> pdb=" O ASP C 493 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP C 493 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 475 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 328 through 332 removed outlier: 6.312A pdb=" N GLN C 350 " --> pdb=" O THR C 433 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 425 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 364 through 368 706 hydrogen bonds defined for protein. 1938 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: 5.97 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 12793 0.99 - 1.20: 13 1.20 - 1.40: 5130 1.40 - 1.61: 7757 1.61 - 1.81: 105 Bond restraints: 25798 Sorted by residual: bond pdb=" C ILE A 142 " pdb=" O ILE A 142 " ideal model delta sigma weight residual 1.248 1.202 0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" NH1 ARG A 531 " pdb="HH12 ARG A 531 " ideal model delta sigma weight residual 0.860 0.787 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" NH1 ARG D 990 " pdb="HH12 ARG D 990 " ideal model delta sigma weight residual 0.860 0.794 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NH1 ARG A 152 " pdb="HH12 ARG A 152 " ideal model delta sigma weight residual 0.860 0.797 0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" NH1 ARG A 399 " pdb="HH12 ARG A 399 " ideal model delta sigma weight residual 0.860 0.798 0.062 2.00e-02 2.50e+03 9.48e+00 ... (remaining 25793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 46691 7.09 - 14.18: 29 14.18 - 21.27: 17 21.27 - 28.35: 14 28.35 - 35.44: 12 Bond angle restraints: 46763 Sorted by residual: angle pdb=" CZ ARG A 266 " pdb=" NH1 ARG A 266 " pdb="HH12 ARG A 266 " ideal model delta sigma weight residual 120.00 155.44 -35.44 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N TRP C 233 " pdb=" CA TRP C 233 " pdb=" HA TRP C 233 " ideal model delta sigma weight residual 110.00 74.97 35.03 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CB TRP C 233 " pdb=" CA TRP C 233 " pdb=" HA TRP C 233 " ideal model delta sigma weight residual 109.00 74.24 34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C TRP C 233 " pdb=" CA TRP C 233 " pdb=" HA TRP C 233 " ideal model delta sigma weight residual 109.00 74.87 34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" CZ ARG A 92 " pdb=" NH1 ARG A 92 " pdb="HH12 ARG A 92 " ideal model delta sigma weight residual 120.00 153.98 -33.98 3.00e+00 1.11e-01 1.28e+02 ... (remaining 46758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 10411 17.68 - 35.36: 1091 35.36 - 53.05: 387 53.05 - 70.73: 120 70.73 - 88.41: 34 Dihedral angle restraints: 12043 sinusoidal: 6745 harmonic: 5298 Sorted by residual: dihedral pdb=" CD ARG C 393 " pdb=" NE ARG C 393 " pdb=" CZ ARG C 393 " pdb=" NH1 ARG C 393 " ideal model delta sinusoidal sigma weight residual 0.00 81.26 -81.26 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CD ARG D1003 " pdb=" NE ARG D1003 " pdb=" CZ ARG D1003 " pdb=" NH1 ARG D1003 " ideal model delta sinusoidal sigma weight residual 0.00 -80.58 80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CD ARG A 92 " pdb=" NE ARG A 92 " pdb=" CZ ARG A 92 " pdb=" NH1 ARG A 92 " ideal model delta sinusoidal sigma weight residual 0.00 77.77 -77.77 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 12040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1688 0.067 - 0.135: 293 0.135 - 0.202: 27 0.202 - 0.269: 2 0.269 - 0.337: 1 Chirality restraints: 2011 Sorted by residual: chirality pdb=" CA TRP C 233 " pdb=" N TRP C 233 " pdb=" C TRP C 233 " pdb=" CB TRP C 233 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 294 " pdb=" N VAL A 294 " pdb=" C VAL A 294 " pdb=" CB VAL A 294 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2008 not shown) Planarity restraints: 3928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 323 " 0.008 9.50e-02 1.11e+02 2.50e-01 1.41e+03 pdb=" NE ARG B 323 " -0.082 2.00e-02 2.50e+03 pdb=" CZ ARG B 323 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 323 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG B 323 " 0.054 2.00e-02 2.50e+03 pdb="HH11 ARG B 323 " 0.430 2.00e-02 2.50e+03 pdb="HH12 ARG B 323 " -0.500 2.00e-02 2.50e+03 pdb="HH21 ARG B 323 " -0.143 2.00e-02 2.50e+03 pdb="HH22 ARG B 323 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 320 " -0.506 9.50e-02 1.11e+02 2.22e-01 5.00e+02 pdb=" NE ARG B 320 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 320 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG B 320 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG B 320 " 0.035 2.00e-02 2.50e+03 pdb="HH11 ARG B 320 " 0.264 2.00e-02 2.50e+03 pdb="HH12 ARG B 320 " -0.289 2.00e-02 2.50e+03 pdb="HH21 ARG B 320 " -0.058 2.00e-02 2.50e+03 pdb="HH22 ARG B 320 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 316 " 0.355 9.50e-02 1.11e+02 1.78e-01 4.16e+02 pdb=" NE ARG B 316 " 0.091 2.00e-02 2.50e+03 pdb=" CZ ARG B 316 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG B 316 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 316 " -0.036 2.00e-02 2.50e+03 pdb="HH11 ARG B 316 " -0.265 2.00e-02 2.50e+03 pdb="HH12 ARG B 316 " 0.265 2.00e-02 2.50e+03 pdb="HH21 ARG B 316 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 316 " -0.100 2.00e-02 2.50e+03 ... (remaining 3925 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1122 2.16 - 2.77: 50639 2.77 - 3.38: 72465 3.38 - 3.99: 97191 3.99 - 4.60: 149043 Nonbonded interactions: 370460 Sorted by model distance: nonbonded pdb=" OH TYR B 381 " pdb=" HG SER B 439 " model vdw 1.553 2.450 nonbonded pdb="HD22 ASN B 382 " pdb=" OE2 GLU B 431 " model vdw 1.571 2.450 nonbonded pdb=" HZ3 LYS A 471 " pdb=" O GLY A 473 " model vdw 1.575 2.450 nonbonded pdb=" H TRP C 233 " pdb=" HA TRP C 233 " model vdw 1.579 1.816 nonbonded pdb=" HZ2 LYS A 47 " pdb=" O HOH A 702 " model vdw 1.594 2.450 ... (remaining 370455 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 554 or (resid 601 and (name N9 or name C8 or nam \ e N7 or name C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C \ 4 or name H8 or name H61 or name H62 or name H2 )))) selection = (chain 'B' and (resid 2 through 554 or (resid 601 and (name N9 or name C8 or nam \ e N7 or name C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C \ 4 or name H8 or name H61 or name H62 or name H2 )))) selection = (chain 'C' and (resid 2 through 554 or (resid 601 and (name N9 or name C8 or nam \ e N7 or name C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C \ 4 or name H8 or name H61 or name H62 or name H2 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.710 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12983 Z= 0.261 Angle : 0.827 8.889 17577 Z= 0.511 Chirality : 0.051 0.337 2011 Planarity : 0.039 0.482 2328 Dihedral : 15.206 88.409 4840 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.37 % Allowed : 0.75 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.19), residues: 1676 helix: -1.22 (0.20), residues: 562 sheet: 0.23 (0.26), residues: 378 loop : -1.17 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.141 0.012 ARG A 409 TYR 0.021 0.002 TYR C 381 PHE 0.038 0.003 PHE C 494 TRP 0.016 0.002 TRP C 231 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00464 (12983) covalent geometry : angle 0.82684 (17577) hydrogen bonds : bond 0.11954 ( 706) hydrogen bonds : angle 6.66164 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.6943 (mt) cc_final: 0.6740 (mt) REVERT: A 393 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8142 (ttp-110) REVERT: A 420 ASP cc_start: 0.7975 (t70) cc_final: 0.7756 (t0) REVERT: B 183 GLU cc_start: 0.8395 (tt0) cc_final: 0.8131 (tt0) REVERT: B 217 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7898 (ttp-110) REVERT: C 107 MET cc_start: 0.8440 (mmt) cc_final: 0.8139 (mmt) REVERT: C 263 LYS cc_start: 0.8229 (tptm) cc_final: 0.7980 (tptm) REVERT: C 267 TYR cc_start: 0.8833 (m-80) cc_final: 0.8626 (m-80) REVERT: C 308 GLU cc_start: 0.8039 (tp30) cc_final: 0.7679 (tp30) outliers start: 5 outliers final: 2 residues processed: 198 average time/residue: 1.9595 time to fit residues: 412.4853 Evaluate side-chains 132 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN B 526 GLN C 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.067683 restraints weight = 59540.467| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.43 r_work: 0.2756 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12983 Z= 0.243 Angle : 0.664 10.259 17577 Z= 0.353 Chirality : 0.046 0.319 2011 Planarity : 0.009 0.322 2328 Dihedral : 4.902 47.851 1815 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.34 % Allowed : 8.06 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1676 helix: 0.64 (0.21), residues: 562 sheet: 0.71 (0.26), residues: 381 loop : -0.65 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1003 TYR 0.022 0.002 TYR B 381 PHE 0.028 0.002 PHE A 212 TRP 0.009 0.001 TRP C 233 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00557 (12983) covalent geometry : angle 0.66426 (17577) hydrogen bonds : bond 0.04978 ( 706) hydrogen bonds : angle 4.98995 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7617 (p90) cc_final: 0.7389 (p90) REVERT: A 302 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 393 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.7869 (ttp80) REVERT: B 82 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.7973 (mmp80) REVERT: B 183 GLU cc_start: 0.8618 (tt0) cc_final: 0.8387 (tt0) REVERT: B 256 GLN cc_start: 0.8826 (tp40) cc_final: 0.8492 (tp-100) REVERT: B 272 GLU cc_start: 0.8239 (tt0) cc_final: 0.7886 (mp0) REVERT: B 373 ARG cc_start: 0.7545 (mtm110) cc_final: 0.6420 (mmt-90) REVERT: C 107 MET cc_start: 0.8578 (mmt) cc_final: 0.8093 (mmt) REVERT: C 256 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 296 ASP cc_start: 0.7754 (m-30) cc_final: 0.7541 (m-30) REVERT: C 393 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8122 (ttp-110) REVERT: C 400 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7596 (ttm-80) REVERT: C 452 MET cc_start: 0.8898 (mtm) cc_final: 0.8685 (mtm) outliers start: 18 outliers final: 3 residues processed: 144 average time/residue: 1.8568 time to fit residues: 285.0463 Evaluate side-chains 122 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 400 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.067635 restraints weight = 59498.875| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.44 r_work: 0.2778 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12983 Z= 0.173 Angle : 0.554 6.125 17577 Z= 0.291 Chirality : 0.044 0.326 2011 Planarity : 0.006 0.081 2328 Dihedral : 4.311 16.291 1812 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 9.48 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.20), residues: 1676 helix: 1.55 (0.22), residues: 562 sheet: 0.84 (0.26), residues: 387 loop : -0.39 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 304 TYR 0.019 0.002 TYR B 303 PHE 0.026 0.002 PHE A 212 TRP 0.004 0.001 TRP C 231 HIS 0.007 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00399 (12983) covalent geometry : angle 0.55440 (17577) hydrogen bonds : bond 0.04439 ( 706) hydrogen bonds : angle 4.68395 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: A 393 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.7836 (ttp80) REVERT: B 183 GLU cc_start: 0.8720 (tt0) cc_final: 0.8514 (tt0) REVERT: B 256 GLN cc_start: 0.8862 (tp40) cc_final: 0.8512 (tp-100) REVERT: B 272 GLU cc_start: 0.8264 (tt0) cc_final: 0.7891 (mp0) REVERT: B 441 MET cc_start: 0.8425 (mmp) cc_final: 0.8074 (mmp) REVERT: C 256 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 301 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7493 (mm) REVERT: C 400 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7647 (ttt90) REVERT: C 401 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8043 (mt-10) outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 1.7920 time to fit residues: 249.4489 Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.072010 restraints weight = 62116.621| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.48 r_work: 0.2864 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12983 Z= 0.163 Angle : 0.532 5.708 17577 Z= 0.278 Chirality : 0.044 0.330 2011 Planarity : 0.004 0.045 2328 Dihedral : 4.228 15.839 1812 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 9.93 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1676 helix: 2.03 (0.22), residues: 562 sheet: 0.95 (0.26), residues: 387 loop : -0.28 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 373 TYR 0.018 0.002 TYR B 303 PHE 0.022 0.002 PHE C 212 TRP 0.002 0.001 TRP B 231 HIS 0.007 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00384 (12983) covalent geometry : angle 0.53183 (17577) hydrogen bonds : bond 0.04045 ( 706) hydrogen bonds : angle 4.48222 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: A 393 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.7794 (ttp80) REVERT: B 247 LYS cc_start: 0.8426 (ttpp) cc_final: 0.7925 (tmmt) REVERT: B 272 GLU cc_start: 0.8289 (tt0) cc_final: 0.7884 (mp0) REVERT: B 487 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: C 256 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7810 (tm-30) REVERT: C 400 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7633 (ttm-80) REVERT: C 401 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: D 992 LEU cc_start: 0.8972 (mp) cc_final: 0.8753 (mm) outliers start: 12 outliers final: 4 residues processed: 122 average time/residue: 1.7098 time to fit residues: 223.2934 Evaluate side-chains 115 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.070506 restraints weight = 62154.960| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.46 r_work: 0.2863 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12983 Z= 0.220 Angle : 0.547 6.055 17577 Z= 0.287 Chirality : 0.045 0.329 2011 Planarity : 0.004 0.033 2328 Dihedral : 4.320 16.328 1812 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.19 % Allowed : 10.30 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1676 helix: 2.04 (0.22), residues: 562 sheet: 1.00 (0.26), residues: 387 loop : -0.22 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 373 TYR 0.020 0.002 TYR B 381 PHE 0.025 0.002 PHE C 212 TRP 0.002 0.001 TRP B 231 HIS 0.008 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00521 (12983) covalent geometry : angle 0.54747 (17577) hydrogen bonds : bond 0.04301 ( 706) hydrogen bonds : angle 4.53333 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: B 247 LYS cc_start: 0.8436 (ttpp) cc_final: 0.7918 (tmmt) REVERT: B 256 GLN cc_start: 0.8842 (tp40) cc_final: 0.8494 (tp-100) REVERT: B 272 GLU cc_start: 0.8291 (tt0) cc_final: 0.7904 (mp0) REVERT: B 487 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: C 256 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 296 ASP cc_start: 0.7747 (m-30) cc_final: 0.7320 (p0) REVERT: C 400 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7679 (ttt90) REVERT: C 401 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: D 992 LEU cc_start: 0.8976 (mp) cc_final: 0.8768 (mm) outliers start: 16 outliers final: 6 residues processed: 124 average time/residue: 1.6727 time to fit residues: 223.2129 Evaluate side-chains 117 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 148 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.0060 chunk 125 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071238 restraints weight = 62158.967| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.47 r_work: 0.2838 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12983 Z= 0.146 Angle : 0.516 6.022 17577 Z= 0.268 Chirality : 0.044 0.329 2011 Planarity : 0.004 0.072 2328 Dihedral : 4.221 16.070 1812 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.75 % Allowed : 11.19 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.21), residues: 1676 helix: 2.26 (0.22), residues: 562 sheet: 1.03 (0.26), residues: 387 loop : -0.13 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 393 TYR 0.019 0.002 TYR B 303 PHE 0.020 0.001 PHE C 212 TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00343 (12983) covalent geometry : angle 0.51591 (17577) hydrogen bonds : bond 0.03935 ( 706) hydrogen bonds : angle 4.40631 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: A 393 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.7512 (ttp80) REVERT: B 247 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8012 (ttpp) REVERT: B 272 GLU cc_start: 0.8311 (tt0) cc_final: 0.7913 (mp0) REVERT: C 256 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 296 ASP cc_start: 0.7737 (m-30) cc_final: 0.7272 (p0) REVERT: C 400 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7586 (ttm-80) REVERT: C 401 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7842 (mt-10) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 1.6876 time to fit residues: 210.8926 Evaluate side-chains 111 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 60 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072154 restraints weight = 61705.277| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.43 r_work: 0.2845 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12983 Z= 0.129 Angle : 0.502 5.398 17577 Z= 0.261 Chirality : 0.043 0.332 2011 Planarity : 0.003 0.045 2328 Dihedral : 4.083 15.655 1812 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.75 % Allowed : 11.42 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.21), residues: 1676 helix: 2.43 (0.22), residues: 562 sheet: 1.09 (0.26), residues: 387 loop : -0.04 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.020 0.002 TYR B 303 PHE 0.018 0.001 PHE C 212 TRP 0.002 0.000 TRP A 233 HIS 0.009 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00300 (12983) covalent geometry : angle 0.50194 (17577) hydrogen bonds : bond 0.03694 ( 706) hydrogen bonds : angle 4.29400 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: A 393 ARG cc_start: 0.8420 (mtp-110) cc_final: 0.7525 (ttp80) REVERT: B 247 LYS cc_start: 0.8394 (ttpp) cc_final: 0.7994 (ttpp) REVERT: C 256 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 296 ASP cc_start: 0.7773 (m-30) cc_final: 0.7536 (p0) REVERT: C 400 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7612 (ttm-80) REVERT: C 401 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7911 (mt-10) outliers start: 10 outliers final: 6 residues processed: 115 average time/residue: 1.7460 time to fit residues: 215.7950 Evaluate side-chains 109 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.098756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072470 restraints weight = 62189.937| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.44 r_work: 0.2851 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12983 Z= 0.120 Angle : 0.502 6.413 17577 Z= 0.260 Chirality : 0.043 0.332 2011 Planarity : 0.003 0.039 2328 Dihedral : 4.013 15.461 1812 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.75 % Allowed : 11.79 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1676 helix: 2.53 (0.22), residues: 562 sheet: 1.12 (0.26), residues: 387 loop : 0.01 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.020 0.002 TYR B 303 PHE 0.018 0.001 PHE B 212 TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00278 (12983) covalent geometry : angle 0.50197 (17577) hydrogen bonds : bond 0.03622 ( 706) hydrogen bonds : angle 4.25298 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: A 393 ARG cc_start: 0.8412 (mtp-110) cc_final: 0.7552 (ttp80) REVERT: B 12 GLN cc_start: 0.8008 (tt0) cc_final: 0.7482 (tm-30) REVERT: B 247 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8002 (ttpp) REVERT: C 256 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7897 (tm-30) REVERT: C 296 ASP cc_start: 0.7751 (m-30) cc_final: 0.7535 (p0) REVERT: C 400 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7586 (ttm-80) REVERT: C 401 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7858 (mt-10) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 1.8974 time to fit residues: 227.6346 Evaluate side-chains 108 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 60 optimal weight: 0.0470 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073132 restraints weight = 61921.805| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.41 r_work: 0.2874 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12983 Z= 0.106 Angle : 0.502 7.336 17577 Z= 0.258 Chirality : 0.043 0.333 2011 Planarity : 0.003 0.034 2328 Dihedral : 3.948 15.221 1812 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.82 % Allowed : 11.79 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.21), residues: 1676 helix: 2.65 (0.22), residues: 562 sheet: 1.16 (0.26), residues: 387 loop : 0.07 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 269 TYR 0.020 0.001 TYR B 303 PHE 0.017 0.001 PHE B 212 TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00243 (12983) covalent geometry : angle 0.50171 (17577) hydrogen bonds : bond 0.03512 ( 706) hydrogen bonds : angle 4.19082 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8284 (mmmt) REVERT: A 302 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 393 ARG cc_start: 0.8433 (mtp-110) cc_final: 0.7590 (ttp80) REVERT: B 12 GLN cc_start: 0.8024 (tt0) cc_final: 0.7517 (tm-30) REVERT: B 247 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8004 (ttpp) REVERT: C 256 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 400 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7583 (ttm-80) REVERT: C 401 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7862 (mt-10) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 1.9138 time to fit residues: 229.8979 Evaluate side-chains 111 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 104 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.072301 restraints weight = 61567.531| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.41 r_work: 0.2860 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12983 Z= 0.141 Angle : 0.509 10.907 17577 Z= 0.262 Chirality : 0.044 0.332 2011 Planarity : 0.003 0.035 2328 Dihedral : 3.972 15.173 1812 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.82 % Allowed : 11.79 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.21), residues: 1676 helix: 2.67 (0.22), residues: 562 sheet: 1.18 (0.26), residues: 387 loop : 0.08 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.021 0.002 TYR B 303 PHE 0.020 0.001 PHE C 212 TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00333 (12983) covalent geometry : angle 0.50899 (17577) hydrogen bonds : bond 0.03620 ( 706) hydrogen bonds : angle 4.20778 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8262 (mmmt) REVERT: A 302 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: A 393 ARG cc_start: 0.8434 (mtp-110) cc_final: 0.7605 (ttp80) REVERT: B 12 GLN cc_start: 0.8195 (tt0) cc_final: 0.7648 (tm-30) REVERT: B 247 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8002 (ttpp) REVERT: C 256 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 263 LYS cc_start: 0.8288 (tptm) cc_final: 0.8068 (tptm) REVERT: C 400 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7565 (ttm-80) REVERT: C 401 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7909 (mt-10) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 1.8741 time to fit residues: 227.2142 Evaluate side-chains 112 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 115 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073112 restraints weight = 61665.569| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.41 r_work: 0.2873 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12983 Z= 0.109 Angle : 0.498 9.736 17577 Z= 0.257 Chirality : 0.044 0.333 2011 Planarity : 0.003 0.032 2328 Dihedral : 3.907 15.059 1812 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.75 % Allowed : 11.94 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.21), residues: 1676 helix: 2.77 (0.22), residues: 562 sheet: 1.20 (0.26), residues: 387 loop : 0.12 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.021 0.001 TYR B 303 PHE 0.018 0.001 PHE B 212 TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00252 (12983) covalent geometry : angle 0.49781 (17577) hydrogen bonds : bond 0.03443 ( 706) hydrogen bonds : angle 4.13633 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10145.44 seconds wall clock time: 171 minutes 55.61 seconds (10315.61 seconds total)