Starting phenix.real_space_refine on Sun Jun 22 07:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh3_53153/06_2025/9qh3_53153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh3_53153/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qh3_53153/06_2025/9qh3_53153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh3_53153/06_2025/9qh3_53153.map" model { file = "/net/cci-nas-00/data/ceres_data/9qh3_53153/06_2025/9qh3_53153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh3_53153/06_2025/9qh3_53153.cif" } resolution = 2.4 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= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.37, per 1000 atoms: 0.48 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: 6.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.23 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: 14.23 Time building geometry restraints manager: 7.37 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: 2.430 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: 0.420 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.500 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:18.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.400 ------------------------------------------------------------------------------- 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 : 5.24 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 (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: -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 TRP 0.016 0.002 TRP C 231 HIS 0.004 0.001 HIS B 488 PHE 0.038 0.003 PHE C 494 TYR 0.021 0.002 TYR C 381 ARG 0.141 0.012 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.11954 ( 706) hydrogen bonds : angle 6.66164 ( 1938) covalent geometry : bond 0.00464 (12983) covalent geometry : angle 0.82684 (17577) *********************** 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 : 4.546 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: 4.3612 time to fit residues: 928.3118 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 : 1.806 ------------------------------------------------------------------------------- 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 141 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 97 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.068192 restraints weight = 59323.194| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.43 r_work: 0.2749 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12983 Z= 0.225 Angle : 0.639 10.206 17577 Z= 0.340 Chirality : 0.046 0.322 2011 Planarity : 0.010 0.336 2328 Dihedral : 4.853 51.663 1815 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.12 % Allowed : 7.91 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.20), residues: 1676 helix: 0.71 (0.21), residues: 559 sheet: 0.69 (0.26), residues: 381 loop : -0.67 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 233 HIS 0.006 0.001 HIS A 488 PHE 0.027 0.002 PHE C 212 TYR 0.021 0.002 TYR B 303 ARG 0.020 0.002 ARG D1003 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 706) hydrogen bonds : angle 5.02204 ( 1938) covalent geometry : bond 0.00508 (12983) covalent geometry : angle 0.63912 (17577) *********************** 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: 15 poor density : 137 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7670 (p90) cc_final: 0.7437 (p90) REVERT: A 302 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: A 393 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.7907 (ttp80) REVERT: B 82 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.7985 (mmp80) REVERT: B 183 GLU cc_start: 0.8627 (tt0) cc_final: 0.8396 (tt0) REVERT: B 256 GLN cc_start: 0.8832 (tp40) cc_final: 0.8486 (tp-100) REVERT: B 272 GLU cc_start: 0.8255 (tt0) cc_final: 0.7900 (mp0) REVERT: B 373 ARG cc_start: 0.7583 (mtm110) cc_final: 0.6452 (mmt-90) REVERT: B 441 MET cc_start: 0.8456 (mmp) cc_final: 0.8199 (mmp) REVERT: C 107 MET cc_start: 0.8613 (mmt) cc_final: 0.8206 (mmt) REVERT: C 256 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 296 ASP cc_start: 0.7765 (m-30) cc_final: 0.7555 (m-30) REVERT: C 400 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7605 (ttm-80) REVERT: C 452 MET cc_start: 0.8938 (mtm) cc_final: 0.8672 (mtm) outliers start: 15 outliers final: 4 residues processed: 146 average time/residue: 3.6217 time to fit residues: 568.5497 Evaluate side-chains 124 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 993 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068488 restraints weight = 58748.263| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.47 r_work: 0.2788 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12983 Z= 0.136 Angle : 0.538 5.221 17577 Z= 0.282 Chirality : 0.044 0.329 2011 Planarity : 0.005 0.074 2328 Dihedral : 4.189 15.525 1812 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.75 % Allowed : 9.40 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.20), residues: 1676 helix: 1.57 (0.22), residues: 562 sheet: 0.86 (0.26), residues: 384 loop : -0.39 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 233 HIS 0.007 0.001 HIS A 488 PHE 0.023 0.002 PHE A 212 TYR 0.019 0.002 TYR B 303 ARG 0.004 0.000 ARG D1003 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 706) hydrogen bonds : angle 4.68155 ( 1938) covalent geometry : bond 0.00307 (12983) covalent geometry : angle 0.53800 (17577) *********************** 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 134 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: A 393 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.7843 (ttp80) REVERT: B 82 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.8031 (mmp80) REVERT: B 183 GLU cc_start: 0.8686 (tt0) cc_final: 0.8432 (tt0) REVERT: B 256 GLN cc_start: 0.8845 (tp40) cc_final: 0.8488 (tp-100) REVERT: B 272 GLU cc_start: 0.8272 (tt0) cc_final: 0.7905 (mp0) REVERT: C 107 MET cc_start: 0.8579 (mmt) cc_final: 0.8093 (mmt) REVERT: C 256 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 400 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7642 (ttt90) REVERT: C 401 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7995 (mt-10) outliers start: 10 outliers final: 3 residues processed: 132 average time/residue: 3.4040 time to fit residues: 483.7914 Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain B residue 440 SER 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 44 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.092750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.066921 restraints weight = 59966.463| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.43 r_work: 0.2766 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12983 Z= 0.195 Angle : 0.554 5.141 17577 Z= 0.291 Chirality : 0.045 0.326 2011 Planarity : 0.004 0.049 2328 Dihedral : 4.275 15.777 1812 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.90 % Allowed : 10.07 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.21), residues: 1676 helix: 2.00 (0.22), residues: 562 sheet: 0.93 (0.26), residues: 387 loop : -0.29 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 233 HIS 0.008 0.001 HIS A 488 PHE 0.025 0.002 PHE C 212 TYR 0.020 0.002 TYR B 381 ARG 0.006 0.001 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 706) hydrogen bonds : angle 4.54199 ( 1938) covalent geometry : bond 0.00460 (12983) covalent geometry : angle 0.55439 (17577) *********************** 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 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: A 393 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.7819 (ttp80) REVERT: B 82 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8036 (mmp80) REVERT: B 183 GLU cc_start: 0.8712 (tt0) cc_final: 0.8487 (tt0) REVERT: B 247 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8008 (ttpp) REVERT: B 272 GLU cc_start: 0.8287 (tt0) cc_final: 0.7889 (mp0) REVERT: C 256 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 393 ARG cc_start: 0.8540 (ptm160) cc_final: 0.8309 (ptm160) REVERT: C 400 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7671 (ttt90) REVERT: C 401 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: D 992 LEU cc_start: 0.8943 (mp) cc_final: 0.8726 (mm) outliers start: 12 outliers final: 3 residues processed: 127 average time/residue: 3.5105 time to fit residues: 479.4997 Evaluate side-chains 117 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 401 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.098519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072276 restraints weight = 61968.119| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.43 r_work: 0.2859 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12983 Z= 0.155 Angle : 0.519 5.281 17577 Z= 0.271 Chirality : 0.044 0.327 2011 Planarity : 0.004 0.032 2328 Dihedral : 4.166 15.586 1812 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.75 % Allowed : 10.45 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.21), residues: 1676 helix: 2.17 (0.22), residues: 562 sheet: 1.01 (0.26), residues: 387 loop : -0.17 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 231 HIS 0.008 0.001 HIS A 488 PHE 0.021 0.002 PHE C 212 TYR 0.020 0.002 TYR B 303 ARG 0.004 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 706) hydrogen bonds : angle 4.42989 ( 1938) covalent geometry : bond 0.00359 (12983) covalent geometry : angle 0.51871 (17577) *********************** 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 126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: A 393 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.7860 (ttp80) REVERT: B 82 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.8001 (mmp80) REVERT: B 247 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8013 (ttpp) REVERT: B 272 GLU cc_start: 0.8293 (tt0) cc_final: 0.7890 (mp0) REVERT: C 256 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 296 ASP cc_start: 0.7740 (m-30) cc_final: 0.7320 (p0) REVERT: C 308 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7325 (tp30) REVERT: C 393 ARG cc_start: 0.8491 (ptm160) cc_final: 0.8221 (ttp-110) REVERT: C 400 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7638 (ttm-80) REVERT: C 401 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7982 (mt-10) outliers start: 10 outliers final: 3 residues processed: 123 average time/residue: 3.2606 time to fit residues: 433.7372 Evaluate side-chains 117 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 401 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 14 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.098283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072044 restraints weight = 61841.321| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.41 r_work: 0.2851 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12983 Z= 0.162 Angle : 0.517 5.834 17577 Z= 0.269 Chirality : 0.044 0.330 2011 Planarity : 0.004 0.032 2328 Dihedral : 4.149 15.541 1812 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.82 % Allowed : 10.75 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.21), residues: 1676 helix: 2.30 (0.22), residues: 562 sheet: 1.06 (0.26), residues: 387 loop : -0.10 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 231 HIS 0.008 0.001 HIS A 488 PHE 0.022 0.002 PHE C 212 TYR 0.020 0.002 TYR B 303 ARG 0.003 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 706) hydrogen bonds : angle 4.37564 ( 1938) covalent geometry : bond 0.00384 (12983) covalent geometry : angle 0.51673 (17577) *********************** 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 128 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 393 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.7779 (ttp80) REVERT: B 82 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.7992 (mmp80) REVERT: B 247 LYS cc_start: 0.8390 (ttpp) cc_final: 0.8001 (ttpp) REVERT: B 272 GLU cc_start: 0.8324 (tt0) cc_final: 0.7913 (mp0) REVERT: C 256 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7816 (tm-30) REVERT: C 296 ASP cc_start: 0.7799 (m-30) cc_final: 0.7360 (p0) REVERT: C 400 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7644 (ttm-80) REVERT: C 401 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7966 (mt-10) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 3.4012 time to fit residues: 462.1110 Evaluate side-chains 117 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 520 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.097793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071540 restraints weight = 62206.709| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.42 r_work: 0.2845 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12983 Z= 0.176 Angle : 0.524 6.335 17577 Z= 0.273 Chirality : 0.044 0.331 2011 Planarity : 0.004 0.034 2328 Dihedral : 4.151 15.682 1812 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.67 % Allowed : 11.42 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.21), residues: 1676 helix: 2.34 (0.22), residues: 562 sheet: 1.08 (0.26), residues: 387 loop : -0.07 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 231 HIS 0.008 0.001 HIS A 488 PHE 0.022 0.002 PHE C 212 TYR 0.019 0.002 TYR B 303 ARG 0.003 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 706) hydrogen bonds : angle 4.37840 ( 1938) covalent geometry : bond 0.00418 (12983) covalent geometry : angle 0.52449 (17577) *********************** 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 118 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: A 393 ARG cc_start: 0.8423 (mtp-110) cc_final: 0.7791 (ttp80) REVERT: B 247 LYS cc_start: 0.8399 (ttpp) cc_final: 0.7999 (ttpp) REVERT: B 272 GLU cc_start: 0.8315 (tt0) cc_final: 0.7923 (mp0) REVERT: C 256 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 296 ASP cc_start: 0.7825 (m-30) cc_final: 0.7422 (p0) REVERT: C 393 ARG cc_start: 0.8393 (ptm160) cc_final: 0.8170 (ttt-90) REVERT: C 400 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7619 (ttm-80) REVERT: C 401 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7919 (mt-10) outliers start: 9 outliers final: 6 residues processed: 117 average time/residue: 3.3987 time to fit residues: 428.1034 Evaluate side-chains 111 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 B residue 301 LEU 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 132 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.098309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072061 restraints weight = 61732.709| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.42 r_work: 0.2855 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3785 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= 0.139 Angle : 0.515 8.103 17577 Z= 0.266 Chirality : 0.044 0.331 2011 Planarity : 0.003 0.034 2328 Dihedral : 4.085 15.564 1812 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.67 % Allowed : 11.57 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.21), residues: 1676 helix: 2.46 (0.22), residues: 562 sheet: 1.12 (0.26), residues: 387 loop : -0.02 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 233 HIS 0.009 0.001 HIS A 488 PHE 0.019 0.001 PHE C 212 TYR 0.020 0.002 TYR B 303 ARG 0.003 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 706) hydrogen bonds : angle 4.30919 ( 1938) covalent geometry : bond 0.00326 (12983) covalent geometry : angle 0.51456 (17577) *********************** 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 114 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 415 MET cc_start: 0.8833 (mmm) cc_final: 0.8533 (mmt) REVERT: B 247 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8000 (ttpp) REVERT: C 256 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 296 ASP cc_start: 0.7819 (m-30) cc_final: 0.7590 (p0) REVERT: C 393 ARG cc_start: 0.8391 (ptm160) cc_final: 0.8158 (ttp-110) REVERT: C 400 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7596 (ttm-80) REVERT: C 401 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7897 (mt-10) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 3.3788 time to fit residues: 408.5303 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 : 1.987 ------------------------------------------------------------------------------- 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 B residue 396 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 246 ILE 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 148 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.097956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.071671 restraints weight = 62473.258| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.44 r_work: 0.2837 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12983 Z= 0.159 Angle : 0.521 9.544 17577 Z= 0.269 Chirality : 0.044 0.331 2011 Planarity : 0.004 0.096 2328 Dihedral : 4.094 15.543 1812 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.60 % Allowed : 11.87 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.21), residues: 1676 helix: 2.48 (0.22), residues: 562 sheet: 1.14 (0.26), residues: 387 loop : -0.01 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 PHE 0.021 0.001 PHE C 212 TYR 0.021 0.002 TYR B 303 ARG 0.003 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 706) hydrogen bonds : angle 4.31321 ( 1938) covalent geometry : bond 0.00377 (12983) covalent geometry : angle 0.52109 (17577) *********************** 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 112 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 393 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.7516 (ttp80) REVERT: B 12 GLN cc_start: 0.8029 (tt0) cc_final: 0.7480 (tm-30) REVERT: B 247 LYS cc_start: 0.8391 (ttpp) cc_final: 0.7996 (ttpp) REVERT: C 256 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 296 ASP cc_start: 0.7819 (m-30) cc_final: 0.7591 (p0) REVERT: C 393 ARG cc_start: 0.8377 (ptm160) cc_final: 0.8145 (ttp-110) REVERT: C 400 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7591 (ttm-80) REVERT: C 401 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7888 (mt-10) outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 3.4494 time to fit residues: 412.4471 Evaluate side-chains 110 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 2.407 ------------------------------------------------------------------------------- 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 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 139 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.097936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.071684 restraints weight = 61897.128| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.42 r_work: 0.2837 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12983 Z= 0.158 Angle : 0.515 8.389 17577 Z= 0.267 Chirality : 0.044 0.330 2011 Planarity : 0.004 0.061 2328 Dihedral : 4.085 15.636 1812 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.67 % Allowed : 11.94 % 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 (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: 1.70 (0.21), residues: 1676 helix: 2.54 (0.22), residues: 562 sheet: 1.17 (0.26), residues: 387 loop : 0.01 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 233 HIS 0.008 0.001 HIS A 488 PHE 0.021 0.001 PHE C 212 TYR 0.021 0.002 TYR B 303 ARG 0.009 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 706) hydrogen bonds : angle 4.29720 ( 1938) covalent geometry : bond 0.00373 (12983) covalent geometry : angle 0.51519 (17577) ********************** 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 115 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 393 ARG cc_start: 0.8466 (mtp-110) cc_final: 0.7618 (ttp80) REVERT: A 415 MET cc_start: 0.8806 (mmm) cc_final: 0.8476 (mmt) REVERT: B 12 GLN cc_start: 0.8172 (tt0) cc_final: 0.7594 (tm-30) REVERT: B 247 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7974 (ttpp) REVERT: B 256 GLN cc_start: 0.8828 (tp40) cc_final: 0.8466 (tp-100) REVERT: C 256 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 263 LYS cc_start: 0.8305 (tptm) cc_final: 0.8087 (tptm) REVERT: C 393 ARG cc_start: 0.8355 (ptm160) cc_final: 0.8124 (ttt-90) REVERT: C 400 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7580 (ttm-80) REVERT: C 401 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7864 (mt-10) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 3.9248 time to fit residues: 483.0816 Evaluate side-chains 110 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 2.814 ------------------------------------------------------------------------------- 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 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 124 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.093514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067986 restraints weight = 59949.167| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.41 r_work: 0.2729 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12983 Z= 0.130 Angle : 0.509 9.077 17577 Z= 0.263 Chirality : 0.044 0.331 2011 Planarity : 0.004 0.073 2328 Dihedral : 4.012 15.274 1812 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.52 % Allowed : 12.16 % 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 (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: 1.81 (0.21), residues: 1676 helix: 2.66 (0.22), residues: 562 sheet: 1.20 (0.26), residues: 387 loop : 0.06 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 233 HIS 0.009 0.001 HIS A 488 PHE 0.018 0.001 PHE B 212 TYR 0.020 0.002 TYR B 303 ARG 0.011 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 706) hydrogen bonds : angle 4.22460 ( 1938) covalent geometry : bond 0.00304 (12983) covalent geometry : angle 0.50851 (17577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19953.16 seconds wall clock time: 341 minutes 35.86 seconds (20495.86 seconds total)