Starting phenix.real_space_refine on Sun May 3 14:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v8a_64832/05_2026/9v8a_64832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v8a_64832/05_2026/9v8a_64832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v8a_64832/05_2026/9v8a_64832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v8a_64832/05_2026/9v8a_64832.map" model { file = "/net/cci-nas-00/data/ceres_data/9v8a_64832/05_2026/9v8a_64832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v8a_64832/05_2026/9v8a_64832.cif" } resolution = 2.66 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 6 5.21 5 S 30 5.16 5 C 8316 2.51 5 N 2472 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13557 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6096 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6096 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Chain: "b" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "c" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.54, per 1000 atoms: 0.26 Number of scatterers: 13557 At special positions: 0 Unit cell: (90.206, 106.375, 126.799, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 65 15.00 Mg 6 11.99 O 2668 8.00 N 2472 7.00 C 8316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 33.5% alpha, 24.1% beta 21 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.848A pdb=" N ALA A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.735A pdb=" N ASN A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.885A pdb=" N ARG A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.388A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 749 through 763 removed outlier: 4.193A pdb=" N SER A 755 " --> pdb=" O THR A 751 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 54 Processing helix chain 'a' and resid 109 through 130 Processing helix chain 'a' and resid 195 through 202 Processing helix chain 'a' and resid 203 through 208 removed outlier: 3.521A pdb=" N SER a 208 " --> pdb=" O HIS a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 254 through 263 Processing helix chain 'a' and resid 299 through 304 Processing helix chain 'a' and resid 312 through 325 Processing helix chain 'a' and resid 360 through 362 No H-bonds generated for 'chain 'a' and resid 360 through 362' Processing helix chain 'a' and resid 372 through 392 removed outlier: 4.140A pdb=" N MET a 385 " --> pdb=" O ARG a 381 " (cutoff:3.500A) Processing helix chain 'a' and resid 411 through 431 Processing helix chain 'a' and resid 447 through 450 Processing helix chain 'a' and resid 451 through 464 Processing helix chain 'a' and resid 482 through 491 Processing helix chain 'a' and resid 501 through 510 Processing helix chain 'a' and resid 516 through 530 removed outlier: 3.623A pdb=" N ARG a 520 " --> pdb=" O GLY a 516 " (cutoff:3.500A) Processing helix chain 'a' and resid 587 through 606 Processing helix chain 'a' and resid 621 through 639 Processing helix chain 'a' and resid 697 through 703 Processing helix chain 'a' and resid 723 through 734 Processing helix chain 'a' and resid 749 through 763 removed outlier: 4.156A pdb=" N SER a 755 " --> pdb=" O THR a 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.521A pdb=" N LEU A 6 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER A 671 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.642A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.917A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 21 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 101 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 23 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU A 99 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 25 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 7.580A pdb=" N ALA A 272 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 234 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A 276 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 232 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 442 removed outlier: 6.861A pdb=" N LEU A 402 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 440 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 404 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR A 442 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR A 406 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 573 removed outlier: 6.401A pdb=" N PHE A 545 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS A 615 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET A 547 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASP A 617 " --> pdb=" O MET A 547 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 549 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 344 through 346 removed outlier: 3.550A pdb=" N PHE a 344 " --> pdb=" O ALA a 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU a 6 " --> pdb=" O THR a 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU a 665 " --> pdb=" O SER a 671 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER a 671 " --> pdb=" O LEU a 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 135 through 139 removed outlier: 6.591A pdb=" N LEU a 142 " --> pdb=" O LYS a 138 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG a 162 " --> pdb=" O ARG a 145 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS a 174 " --> pdb=" O LEU a 171 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL a 330 " --> pdb=" O LEU a 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 58 through 60 removed outlier: 3.827A pdb=" N ALA a 67 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL a 25 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG a 90 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 284 through 287 removed outlier: 7.727A pdb=" N ALA a 272 " --> pdb=" O THR a 236 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG a 276 " --> pdb=" O PHE a 232 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE a 232 " --> pdb=" O ARG a 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 244 through 247 Processing sheet with id=AB5, first strand: chain 'a' and resid 364 through 365 Processing sheet with id=AB6, first strand: chain 'a' and resid 436 through 442 removed outlier: 7.081A pdb=" N LEU a 402 " --> pdb=" O ARG a 438 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE a 440 " --> pdb=" O LEU a 402 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU a 404 " --> pdb=" O ILE a 440 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR a 442 " --> pdb=" O LEU a 404 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR a 406 " --> pdb=" O TYR a 442 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP a 401 " --> pdb=" O LEU a 470 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL a 472 " --> pdb=" O ASP a 401 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL a 403 " --> pdb=" O VAL a 472 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL a 474 " --> pdb=" O VAL a 403 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU a 405 " --> pdb=" O VAL a 474 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 568 through 573 removed outlier: 6.375A pdb=" N PHE a 545 " --> pdb=" O VAL a 613 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS a 615 " --> pdb=" O PHE a 545 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET a 547 " --> pdb=" O HIS a 615 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP a 617 " --> pdb=" O MET a 547 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL a 549 " --> pdb=" O ASP a 617 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU a 612 " --> pdb=" O GLY a 648 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL a 650 " --> pdb=" O LEU a 612 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL a 614 " --> pdb=" O VAL a 650 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL a 652 " --> pdb=" O VAL a 614 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG a 616 " --> pdb=" O VAL a 652 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL a 649 " --> pdb=" O THR a 714 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU a 687 " --> pdb=" O LEU a 683 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER a 679 " --> pdb=" O THR a 691 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3657 1.33 - 1.45: 2684 1.45 - 1.57: 7457 1.57 - 1.69: 126 1.69 - 1.81: 46 Bond restraints: 13970 Sorted by residual: bond pdb=" CA GLY A 172 " pdb=" C GLY A 172 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.79e+00 bond pdb=" N GLY A 172 " pdb=" CA GLY A 172 " ideal model delta sigma weight residual 1.464 1.447 0.017 1.12e-02 7.97e+03 2.36e+00 bond pdb=" C VAL a 87 " pdb=" N PRO a 88 " ideal model delta sigma weight residual 1.340 1.379 -0.038 2.76e-02 1.31e+03 1.94e+00 bond pdb=" N ASP A 329 " pdb=" CA ASP A 329 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.92e+00 bond pdb=" CG GLU a 460 " pdb=" CD GLU a 460 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 13965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 18797 1.49 - 2.97: 392 2.97 - 4.46: 48 4.46 - 5.95: 7 5.95 - 7.43: 2 Bond angle restraints: 19246 Sorted by residual: angle pdb=" C VAL A 87 " pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta sigma weight residual 121.65 118.11 3.54 1.01e+00 9.80e-01 1.23e+01 angle pdb=" N GLY a 574 " pdb=" CA GLY a 574 " pdb=" C GLY a 574 " ideal model delta sigma weight residual 113.18 120.61 -7.43 2.37e+00 1.78e-01 9.84e+00 angle pdb=" N GLU a 460 " pdb=" CA GLU a 460 " pdb=" CB GLU a 460 " ideal model delta sigma weight residual 110.28 115.09 -4.81 1.55e+00 4.16e-01 9.63e+00 angle pdb=" C TYR a 389 " pdb=" N GLU a 390 " pdb=" CA GLU a 390 " ideal model delta sigma weight residual 121.52 116.59 4.93 1.84e+00 2.95e-01 7.18e+00 angle pdb=" N ARG A 580 " pdb=" CA ARG A 580 " pdb=" CB ARG A 580 " ideal model delta sigma weight residual 113.65 109.78 3.87 1.47e+00 4.63e-01 6.93e+00 ... (remaining 19241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.09: 7893 28.09 - 56.18: 383 56.18 - 84.28: 63 84.28 - 112.37: 3 112.37 - 140.46: 2 Dihedral angle restraints: 8344 sinusoidal: 3936 harmonic: 4408 Sorted by residual: dihedral pdb=" C4' DT b 13 " pdb=" C3' DT b 13 " pdb=" O3' DT b 13 " pdb=" P DT b 14 " ideal model delta sinusoidal sigma weight residual 220.00 79.54 140.46 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 80.53 139.47 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA GLY a 574 " pdb=" C GLY a 574 " pdb=" N ASP a 575 " pdb=" CA ASP a 575 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1425 0.032 - 0.065: 500 0.065 - 0.097: 111 0.097 - 0.129: 103 0.129 - 0.162: 9 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CA ASP A 329 " pdb=" N ASP A 329 " pdb=" C ASP A 329 " pdb=" CB ASP A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA VAL a 87 " pdb=" N VAL a 87 " pdb=" C VAL a 87 " pdb=" CB VAL a 87 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA GLU A 390 " pdb=" N GLU A 390 " pdb=" C GLU A 390 " pdb=" CB GLU A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2145 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 399 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO a 400 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO a 400 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO a 400 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL a 607 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO a 608 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO a 608 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO a 608 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 691 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 692 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 692 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 692 " -0.018 5.00e-02 4.00e+02 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 77 2.59 - 3.17: 10173 3.17 - 3.75: 20240 3.75 - 4.32: 30229 4.32 - 4.90: 48543 Nonbonded interactions: 109262 Sorted by model distance: nonbonded pdb=" OD2 ASP a 550 " pdb="MG MG a 802 " model vdw 2.016 2.170 nonbonded pdb=" OP1 U c 7 " pdb="MG MG a 802 " model vdw 2.021 2.170 nonbonded pdb="MG MG a 802 " pdb=" O HOH a 902 " model vdw 2.046 2.170 nonbonded pdb=" OD1 ASP A 756 " pdb="MG MG A 803 " model vdw 2.121 2.170 nonbonded pdb=" OP1 U C 7 " pdb="MG MG A 803 " model vdw 2.170 2.170 ... (remaining 109257 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 4 through 802) selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 1 through 17) selection = chain 'b' } ncs_group { reference = chain 'C' selection = (chain 'c' and resid 1 through 15) } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.003 0.038 13970 Z= 0.149 Angle : 0.524 7.434 19246 Z= 0.284 Chirality : 0.041 0.162 2148 Planarity : 0.004 0.038 2295 Dihedral : 15.729 140.461 5504 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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 are not related in a simple way. whole: 0.85 (0.21), residues: 1524 helix: 1.60 (0.23), residues: 476 sheet: 1.31 (0.28), residues: 328 loop : -0.49 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 506 TYR 0.018 0.002 TYR a 380 PHE 0.012 0.001 PHE A 232 TRP 0.017 0.001 TRP A 65 HIS 0.009 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00330 (13970) covalent geometry : angle 0.52442 (19246) hydrogen bonds : bond 0.18934 ( 605) hydrogen bonds : angle 6.74042 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.496 Fit side-chains REVERT: A 485 ASP cc_start: 0.7161 (m-30) cc_final: 0.6918 (m-30) REVERT: a 202 GLU cc_start: 0.6246 (mt-10) cc_final: 0.6046 (mp0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.8547 time to fit residues: 160.3379 Evaluate side-chains 138 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 325 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 449 HIS a 542 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118175 restraints weight = 14390.526| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.79 r_work: 0.3160 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13970 Z= 0.265 Angle : 0.680 8.791 19246 Z= 0.363 Chirality : 0.048 0.180 2148 Planarity : 0.006 0.053 2295 Dihedral : 15.348 143.078 2518 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.60 % Allowed : 7.57 % Favored : 89.83 % 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 are not related in a simple way. whole: 0.63 (0.21), residues: 1524 helix: 1.39 (0.23), residues: 482 sheet: 0.84 (0.26), residues: 396 loop : -0.56 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 22 TYR 0.023 0.002 TYR A 380 PHE 0.016 0.002 PHE a 545 TRP 0.020 0.002 TRP A 136 HIS 0.007 0.002 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00623 (13970) covalent geometry : angle 0.67973 (19246) hydrogen bonds : bond 0.06686 ( 605) hydrogen bonds : angle 5.14227 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.519 Fit side-chains REVERT: A 131 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: A 259 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6979 (mp0) REVERT: A 485 ASP cc_start: 0.7752 (m-30) cc_final: 0.7466 (m-30) REVERT: A 601 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: a 266 VAL cc_start: 0.7137 (t) cc_final: 0.6870 (t) outliers start: 34 outliers final: 11 residues processed: 162 average time/residue: 0.8266 time to fit residues: 143.3518 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 300 ASP Chi-restraints excluded: chain a residue 366 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 251 GLN A 361 ASN A 439 GLN A 576 GLN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS a 521 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121564 restraints weight = 14407.228| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.75 r_work: 0.3213 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13970 Z= 0.138 Angle : 0.534 7.636 19246 Z= 0.290 Chirality : 0.042 0.160 2148 Planarity : 0.005 0.043 2295 Dihedral : 15.046 140.732 2518 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.68 % Allowed : 9.86 % Favored : 88.46 % 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 are not related in a simple way. whole: 0.91 (0.21), residues: 1524 helix: 1.75 (0.23), residues: 482 sheet: 1.17 (0.27), residues: 354 loop : -0.53 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 157 TYR 0.017 0.001 TYR a 380 PHE 0.014 0.001 PHE A 63 TRP 0.014 0.001 TRP A 136 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00305 (13970) covalent geometry : angle 0.53359 (19246) hydrogen bonds : bond 0.04619 ( 605) hydrogen bonds : angle 4.63436 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.524 Fit side-chains REVERT: A 94 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 361 ASN cc_start: 0.8137 (m-40) cc_final: 0.7889 (t0) REVERT: A 425 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: A 485 ASP cc_start: 0.7610 (m-30) cc_final: 0.7310 (m-30) REVERT: a 255 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6668 (mmm-85) REVERT: a 266 VAL cc_start: 0.7072 (t) cc_final: 0.6660 (t) REVERT: a 424 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: a 460 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: a 480 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7556 (mmt90) outliers start: 22 outliers final: 6 residues processed: 159 average time/residue: 0.8443 time to fit residues: 143.3497 Evaluate side-chains 147 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 255 ARG Chi-restraints excluded: chain a residue 424 GLU Chi-restraints excluded: chain a residue 460 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 22 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119185 restraints weight = 14402.478| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.76 r_work: 0.3181 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13970 Z= 0.212 Angle : 0.614 8.331 19246 Z= 0.328 Chirality : 0.045 0.175 2148 Planarity : 0.006 0.046 2295 Dihedral : 15.226 142.561 2518 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.37 % Allowed : 11.54 % Favored : 86.09 % 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 are not related in a simple way. whole: 0.79 (0.21), residues: 1524 helix: 1.60 (0.23), residues: 482 sheet: 1.05 (0.27), residues: 376 loop : -0.57 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 419 TYR 0.022 0.002 TYR A 380 PHE 0.016 0.002 PHE a 545 TRP 0.016 0.002 TRP A 136 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00495 (13970) covalent geometry : angle 0.61395 (19246) hydrogen bonds : bond 0.05741 ( 605) hydrogen bonds : angle 4.74899 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.498 Fit side-chains REVERT: A 91 GLU cc_start: 0.7176 (tt0) cc_final: 0.6826 (tp30) REVERT: A 94 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 131 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8207 (m-40) REVERT: A 165 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (tttt) REVERT: A 361 ASN cc_start: 0.8165 (m-40) cc_final: 0.7897 (t0) REVERT: A 425 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: A 485 ASP cc_start: 0.7677 (m-30) cc_final: 0.7399 (m-30) REVERT: a 99 GLU cc_start: 0.7683 (tp30) cc_final: 0.7255 (tp30) REVERT: a 266 VAL cc_start: 0.7091 (t) cc_final: 0.6849 (t) REVERT: a 417 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7285 (mppt) REVERT: a 460 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: a 480 ARG cc_start: 0.7767 (mmm-85) cc_final: 0.7537 (mmt90) outliers start: 31 outliers final: 9 residues processed: 158 average time/residue: 0.8543 time to fit residues: 144.2706 Evaluate side-chains 148 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 173 ASP Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 460 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118070 restraints weight = 14394.586| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.77 r_work: 0.3165 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13970 Z= 0.213 Angle : 0.617 8.520 19246 Z= 0.330 Chirality : 0.045 0.175 2148 Planarity : 0.006 0.047 2295 Dihedral : 15.240 142.220 2518 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.52 % Allowed : 12.77 % Favored : 84.71 % 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 are not related in a simple way. whole: 0.75 (0.21), residues: 1524 helix: 1.56 (0.23), residues: 482 sheet: 0.88 (0.25), residues: 418 loop : -0.58 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 22 TYR 0.021 0.002 TYR A 380 PHE 0.016 0.002 PHE a 545 TRP 0.017 0.002 TRP A 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd covalent geometry : bond 0.00499 (13970) covalent geometry : angle 0.61736 (19246) hydrogen bonds : bond 0.05683 ( 605) hydrogen bonds : angle 4.73538 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 95 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: A 157 ARG cc_start: 0.8238 (mtp85) cc_final: 0.8037 (mtp85) REVERT: A 165 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8459 (tttt) REVERT: A 361 ASN cc_start: 0.8161 (m-40) cc_final: 0.7888 (t0) REVERT: A 425 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: A 485 ASP cc_start: 0.7658 (m-30) cc_final: 0.7379 (m-30) REVERT: a 99 GLU cc_start: 0.7716 (tp30) cc_final: 0.7261 (tp30) REVERT: a 266 VAL cc_start: 0.7113 (t) cc_final: 0.6852 (t) REVERT: a 417 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7250 (mppt) REVERT: a 460 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: a 480 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7605 (mmt90) outliers start: 33 outliers final: 14 residues processed: 152 average time/residue: 0.8702 time to fit residues: 141.0027 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 314 ASP Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 387 MET Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 687 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121133 restraints weight = 14290.700| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.71 r_work: 0.3206 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13970 Z= 0.130 Angle : 0.526 7.669 19246 Z= 0.285 Chirality : 0.041 0.161 2148 Planarity : 0.005 0.042 2295 Dihedral : 14.962 140.798 2518 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.99 % Allowed : 13.99 % Favored : 84.02 % 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 are not related in a simple way. whole: 1.00 (0.21), residues: 1524 helix: 1.87 (0.24), residues: 480 sheet: 1.16 (0.27), residues: 376 loop : -0.51 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 419 TYR 0.017 0.001 TYR a 380 PHE 0.013 0.001 PHE A 232 TRP 0.013 0.001 TRP A 136 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00284 (13970) covalent geometry : angle 0.52633 (19246) hydrogen bonds : bond 0.04283 ( 605) hydrogen bonds : angle 4.44470 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.494 Fit side-chains REVERT: A 91 GLU cc_start: 0.7140 (tt0) cc_final: 0.6812 (tp30) REVERT: A 94 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7817 (mm) REVERT: A 165 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8364 (tttt) REVERT: A 361 ASN cc_start: 0.8165 (m-40) cc_final: 0.7913 (t0) REVERT: A 425 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 485 ASP cc_start: 0.7566 (m-30) cc_final: 0.7280 (m-30) REVERT: a 99 GLU cc_start: 0.7665 (tp30) cc_final: 0.7268 (tp30) REVERT: a 266 VAL cc_start: 0.7101 (t) cc_final: 0.6849 (t) REVERT: a 460 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: a 512 GLN cc_start: 0.7639 (mp10) cc_final: 0.7433 (mm110) REVERT: a 564 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8473 (tttm) outliers start: 26 outliers final: 12 residues processed: 155 average time/residue: 0.8369 time to fit residues: 138.7216 Evaluate side-chains 152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 314 ASP Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 549 VAL Chi-restraints excluded: chain a residue 564 LYS Chi-restraints excluded: chain a residue 687 GLU Chi-restraints excluded: chain a residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117539 restraints weight = 14354.272| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.66 r_work: 0.3155 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13970 Z= 0.214 Angle : 0.616 8.381 19246 Z= 0.329 Chirality : 0.045 0.178 2148 Planarity : 0.006 0.056 2295 Dihedral : 15.224 142.634 2518 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.14 % Allowed : 14.30 % Favored : 83.56 % 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 are not related in a simple way. whole: 0.78 (0.21), residues: 1524 helix: 1.63 (0.23), residues: 480 sheet: 1.05 (0.27), residues: 376 loop : -0.60 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 419 TYR 0.022 0.002 TYR A 380 PHE 0.016 0.002 PHE a 545 TRP 0.016 0.002 TRP A 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd covalent geometry : bond 0.00501 (13970) covalent geometry : angle 0.61603 (19246) hydrogen bonds : bond 0.05664 ( 605) hydrogen bonds : angle 4.69762 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.493 Fit side-chains REVERT: A 91 GLU cc_start: 0.7095 (tt0) cc_final: 0.6768 (tp30) REVERT: A 94 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7807 (mm) REVERT: A 95 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 165 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8435 (tttt) REVERT: A 361 ASN cc_start: 0.8149 (m-40) cc_final: 0.7909 (t0) REVERT: A 425 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: A 485 ASP cc_start: 0.7629 (m-30) cc_final: 0.7344 (m-30) REVERT: a 99 GLU cc_start: 0.7698 (tp30) cc_final: 0.7264 (tp30) REVERT: a 266 VAL cc_start: 0.7097 (t) cc_final: 0.6836 (t) REVERT: a 460 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6796 (mp0) outliers start: 28 outliers final: 10 residues processed: 155 average time/residue: 0.8286 time to fit residues: 137.5508 Evaluate side-chains 152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 314 ASP Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 687 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 138 optimal weight: 0.0770 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121856 restraints weight = 14162.719| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.89 r_work: 0.3212 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13970 Z= 0.121 Angle : 0.516 7.317 19246 Z= 0.280 Chirality : 0.041 0.160 2148 Planarity : 0.005 0.057 2295 Dihedral : 14.878 140.394 2518 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.99 % Allowed : 15.83 % Favored : 83.18 % 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 are not related in a simple way. whole: 1.09 (0.21), residues: 1524 helix: 1.96 (0.24), residues: 480 sheet: 1.21 (0.27), residues: 376 loop : -0.47 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 419 TYR 0.017 0.001 TYR a 380 PHE 0.013 0.001 PHE A 232 TRP 0.013 0.001 TRP A 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd covalent geometry : bond 0.00264 (13970) covalent geometry : angle 0.51622 (19246) hydrogen bonds : bond 0.03959 ( 605) hydrogen bonds : angle 4.37237 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.448 Fit side-chains REVERT: A 91 GLU cc_start: 0.7081 (tt0) cc_final: 0.6761 (tp30) REVERT: A 94 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7802 (mm) REVERT: A 157 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7848 (mtp180) REVERT: A 165 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8351 (tttt) REVERT: A 271 GLU cc_start: 0.7213 (pm20) cc_final: 0.6424 (tp30) REVERT: A 361 ASN cc_start: 0.8163 (m-40) cc_final: 0.7922 (t0) REVERT: A 485 ASP cc_start: 0.7577 (m-30) cc_final: 0.7277 (m-30) REVERT: a 94 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7814 (mm) REVERT: a 99 GLU cc_start: 0.7664 (tp30) cc_final: 0.7247 (tp30) REVERT: a 126 ASP cc_start: 0.8552 (m-30) cc_final: 0.7850 (m-30) REVERT: a 266 VAL cc_start: 0.7059 (t) cc_final: 0.6809 (t) REVERT: a 460 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: a 506 ARG cc_start: 0.7190 (mtp-110) cc_final: 0.6895 (mtp85) REVERT: a 512 GLN cc_start: 0.7709 (mp10) cc_final: 0.7500 (mm110) outliers start: 13 outliers final: 7 residues processed: 146 average time/residue: 0.7979 time to fit residues: 125.0164 Evaluate side-chains 150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 687 GLU Chi-restraints excluded: chain a residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122023 restraints weight = 14319.916| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.72 r_work: 0.3218 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13970 Z= 0.127 Angle : 0.519 7.352 19246 Z= 0.280 Chirality : 0.041 0.164 2148 Planarity : 0.005 0.060 2295 Dihedral : 14.882 141.075 2518 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.30 % Allowed : 16.06 % Favored : 82.65 % 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 are not related in a simple way. whole: 1.16 (0.21), residues: 1524 helix: 2.00 (0.24), residues: 480 sheet: 1.26 (0.28), residues: 376 loop : -0.43 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG a 419 TYR 0.017 0.001 TYR a 380 PHE 0.013 0.001 PHE A 232 TRP 0.013 0.001 TRP A 136 HIS 0.003 0.001 HIS a 449 Details of bonding type rmsd covalent geometry : bond 0.00281 (13970) covalent geometry : angle 0.51892 (19246) hydrogen bonds : bond 0.04119 ( 605) hydrogen bonds : angle 4.35358 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.523 Fit side-chains REVERT: A 91 GLU cc_start: 0.7061 (tt0) cc_final: 0.6768 (tp30) REVERT: A 94 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 95 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 157 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7800 (mtp180) REVERT: A 165 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8342 (tttt) REVERT: A 256 GLU cc_start: 0.7348 (mp0) cc_final: 0.7004 (pt0) REVERT: A 271 GLU cc_start: 0.7178 (pm20) cc_final: 0.6442 (tp30) REVERT: A 361 ASN cc_start: 0.8147 (m-40) cc_final: 0.7932 (t0) REVERT: A 485 ASP cc_start: 0.7557 (m-30) cc_final: 0.7247 (m-30) REVERT: a 94 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7841 (mm) REVERT: a 99 GLU cc_start: 0.7665 (tp30) cc_final: 0.7263 (tp30) REVERT: a 126 ASP cc_start: 0.8580 (m-30) cc_final: 0.7888 (m-30) REVERT: a 266 VAL cc_start: 0.7052 (t) cc_final: 0.6821 (t) REVERT: a 417 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7229 (mppt) REVERT: a 460 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: a 506 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6902 (mtp85) REVERT: a 676 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7628 (ttm) outliers start: 17 outliers final: 9 residues processed: 149 average time/residue: 0.8094 time to fit residues: 129.2378 Evaluate side-chains 155 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 314 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 676 MET Chi-restraints excluded: chain a residue 687 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117179 restraints weight = 14315.623| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.67 r_work: 0.3154 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13970 Z= 0.239 Angle : 0.647 8.474 19246 Z= 0.343 Chirality : 0.046 0.248 2148 Planarity : 0.006 0.064 2295 Dihedral : 15.287 142.957 2518 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.68 % Allowed : 15.90 % Favored : 82.42 % 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 are not related in a simple way. whole: 0.78 (0.21), residues: 1524 helix: 1.61 (0.23), residues: 480 sheet: 1.10 (0.27), residues: 376 loop : -0.62 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG a 419 TYR 0.024 0.002 TYR A 380 PHE 0.017 0.002 PHE a 545 TRP 0.015 0.002 TRP A 136 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00564 (13970) covalent geometry : angle 0.64665 (19246) hydrogen bonds : bond 0.05994 ( 605) hydrogen bonds : angle 4.74566 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.671 Fit side-chains REVERT: A 91 GLU cc_start: 0.7069 (tt0) cc_final: 0.6770 (tp30) REVERT: A 94 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7813 (mm) REVERT: A 95 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 165 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (tttt) REVERT: A 271 GLU cc_start: 0.7248 (pm20) cc_final: 0.6527 (tp30) REVERT: A 425 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: A 485 ASP cc_start: 0.7650 (m-30) cc_final: 0.7361 (m-30) REVERT: a 99 GLU cc_start: 0.7705 (tp30) cc_final: 0.7265 (tp30) REVERT: a 266 VAL cc_start: 0.7054 (t) cc_final: 0.6804 (t) REVERT: a 417 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7219 (mppt) REVERT: a 460 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: a 506 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6979 (mtp85) outliers start: 22 outliers final: 10 residues processed: 151 average time/residue: 0.8331 time to fit residues: 134.7297 Evaluate side-chains 151 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 314 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 687 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122484 restraints weight = 14418.130| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.70 r_work: 0.3232 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13970 Z= 0.116 Angle : 0.513 7.054 19246 Z= 0.278 Chirality : 0.040 0.159 2148 Planarity : 0.005 0.063 2295 Dihedral : 14.735 140.393 2518 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.84 % Allowed : 17.20 % Favored : 81.96 % 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 are not related in a simple way. whole: 1.13 (0.21), residues: 1524 helix: 2.00 (0.24), residues: 480 sheet: 1.23 (0.27), residues: 376 loop : -0.46 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 419 TYR 0.016 0.001 TYR a 380 PHE 0.013 0.001 PHE A 232 TRP 0.012 0.001 TRP A 136 HIS 0.003 0.001 HIS a 449 Details of bonding type rmsd covalent geometry : bond 0.00251 (13970) covalent geometry : angle 0.51276 (19246) hydrogen bonds : bond 0.03744 ( 605) hydrogen bonds : angle 4.33591 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4974.48 seconds wall clock time: 85 minutes 18.37 seconds (5118.37 seconds total)