Starting phenix.real_space_refine on Fri Jul 3 11:17:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v8a_64832/07_2026/9v8a_64832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v8a_64832/07_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_64832/07_2026/9v8a_64832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v8a_64832/07_2026/9v8a_64832.map" model { file = "/net/cci-nas-00/data/ceres_data/9v8a_64832/07_2026/9v8a_64832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v8a_64832/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2.49, per 1000 atoms: 0.18 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: 0.92 Conformation dependent library (CDL) restraints added in 506.0 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: 1.50 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: 2.67 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C3' DT b 14 " pdb=" C2' DT b 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.53e+00 bond pdb=" C3' DT B 14 " pdb=" C2' DT B 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.31e+00 bond pdb=" C3' DT B 18 " pdb=" C2' DT B 18 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.46e+00 bond pdb=" C3' DT b 16 " pdb=" C2' DT b 16 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.32e+00 ... (remaining 13965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 18712 1.49 - 2.97: 473 2.97 - 4.46: 52 4.46 - 5.95: 7 5.95 - 7.43: 2 Bond angle restraints: 19246 Sorted by residual: angle pdb=" O4' DG b 4 " pdb=" C4' DG b 4 " pdb=" C3' DG b 4 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT B 1 " pdb=" C4 DT B 1 " pdb=" O4 DT B 1 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " pdb=" O4 DT B 18 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT b 16 " pdb=" C4 DT b 16 " pdb=" O4 DT b 16 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT b 6 " pdb=" C4 DT b 6 " pdb=" O4 DT b 6 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (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 - 0.036: 1486 0.036 - 0.072: 438 0.072 - 0.109: 160 0.109 - 0.145: 58 0.145 - 0.181: 6 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C2' C c 5 " pdb=" C3' C c 5 " pdb=" O2' C c 5 " pdb=" C1' C c 5 " both_signs ideal model delta sigma weight residual False -2.62 -2.80 0.18 2.00e-01 2.50e+01 8.18e-01 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=" C2' C C 5 " pdb=" C3' C C 5 " pdb=" O2' C C 5 " pdb=" C1' C C 5 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.43e-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: 1.620 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.260 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:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13970 Z= 0.234 Angle : 0.549 7.434 19246 Z= 0.365 Chirality : 0.043 0.181 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/Z covalent geometry : bond 0.00354 / 0.23 (13970) covalent geometry : angle 0.54926 / 0.36 (19246) hydrogen bonds : bond 0.18934 / 12.29 ( 605) hydrogen bonds : angle 6.74042 / 4.69 ( 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 : 0.305 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: 0.7077 time to fit residues: 133.1431 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 : 0.368 ------------------------------------------------------------------------------- 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: 2.9990 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: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3708 r_free = 0.3708 target = 0.149132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119138 restraints weight = 14382.635| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.84 r_work: 0.3182 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13970 Z= 0.228 Angle : 0.644 8.150 19246 Z= 0.356 Chirality : 0.047 0.205 2148 Planarity : 0.006 0.047 2295 Dihedral : 15.329 145.614 2518 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.14 % Allowed : 7.49 % Favored : 90.37 % 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: 0.72 (0.21), residues: 1524 helix: 1.50 (0.23), residues: 482 sheet: 0.82 (0.25), residues: 400 loop : -0.48 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.021 0.002 TYR A 380 PHE 0.019 0.002 PHE a 545 TRP 0.017 0.002 TRP A 136 HIS 0.008 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (13970) covalent geometry : angle 0.64424 / 0.36 (19246) hydrogen bonds : bond 0.06788 / 4.37 ( 605) hydrogen bonds : angle 5.31987 / 3.71 ( 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 167 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.414 Fit side-chains REVERT: A 259 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6998 (mp0) REVERT: A 485 ASP cc_start: 0.7693 (m-30) cc_final: 0.7394 (m-30) REVERT: A 588 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7209 (ttp-110) REVERT: A 601 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: a 266 VAL cc_start: 0.7132 (t) cc_final: 0.6886 (t) REVERT: a 460 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7147 (mp0) outliers start: 28 outliers final: 10 residues processed: 154 average time/residue: 0.7286 time to fit residues: 120.2074 Evaluate side-chains 148 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP 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 109 SER Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 676 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 147 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 361 ASN A 439 GLN A 646 GLN a 55 GLN a 449 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120147 restraints weight = 14492.122| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.75 r_work: 0.3196 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1059 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= 0.158 Angle : 0.558 7.877 19246 Z= 0.315 Chirality : 0.044 0.168 2148 Planarity : 0.005 0.045 2295 Dihedral : 15.280 144.798 2518 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.76 % Allowed : 9.33 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.21), residues: 1524 helix: 1.67 (0.23), residues: 482 sheet: 1.14 (0.27), residues: 354 loop : -0.54 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.018 0.002 TYR A 380 PHE 0.014 0.001 PHE A 232 TRP 0.015 0.001 TRP A 136 HIS 0.006 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (13970) covalent geometry : angle 0.55763 / 0.31 (19246) hydrogen bonds : bond 0.05443 / 3.50 ( 605) hydrogen bonds : angle 4.88954 / 3.40 ( 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 168 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.377 Fit side-chains REVERT: A 94 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7915 (mm) REVERT: A 259 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7019 (mp0) REVERT: A 425 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: A 485 ASP cc_start: 0.7604 (m-30) cc_final: 0.7298 (m-30) REVERT: A 588 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7167 (ttp-110) REVERT: a 266 VAL cc_start: 0.7120 (t) cc_final: 0.6872 (t) REVERT: a 424 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: a 480 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7489 (mmt90) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 0.6954 time to fit residues: 115.5689 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE 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 298 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain a residue 36 THR 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 366 THR Chi-restraints excluded: chain a residue 418 LEU Chi-restraints excluded: chain a residue 424 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 124 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 361 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120354 restraints weight = 14405.261| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.72 r_work: 0.3199 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13970 Z= 0.183 Angle : 0.580 8.091 19246 Z= 0.324 Chirality : 0.045 0.171 2148 Planarity : 0.005 0.047 2295 Dihedral : 15.295 144.946 2518 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.99 % Allowed : 11.09 % Favored : 86.93 % 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: 0.84 (0.21), residues: 1524 helix: 1.63 (0.23), residues: 482 sheet: 1.07 (0.27), residues: 376 loop : -0.52 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 22 TYR 0.020 0.002 TYR A 380 PHE 0.015 0.002 PHE a 545 TRP 0.015 0.001 TRP A 136 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (13970) covalent geometry : angle 0.58048 / 0.32 (19246) hydrogen bonds : bond 0.05552 / 3.58 ( 605) hydrogen bonds : angle 4.79579 / 3.34 ( 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 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.418 Fit side-chains REVERT: A 94 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 165 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8442 (tttt) REVERT: A 259 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6943 (mp0) REVERT: A 425 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 485 ASP cc_start: 0.7667 (m-30) cc_final: 0.7373 (m-30) REVERT: a 266 VAL cc_start: 0.7114 (t) cc_final: 0.6874 (t) REVERT: a 417 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7274 (mppt) REVERT: a 460 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6896 (mp0) outliers start: 26 outliers final: 13 residues processed: 153 average time/residue: 0.6666 time to fit residues: 109.4478 Evaluate side-chains 152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP 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 298 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain a residue 36 THR 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 222 ASP Chi-restraints excluded: chain a residue 233 VAL Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 676 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.0770 chunk 94 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN A 646 GLN a 449 HIS a 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119610 restraints weight = 14397.836| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.75 r_work: 0.3182 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13970 Z= 0.184 Angle : 0.583 8.304 19246 Z= 0.326 Chirality : 0.045 0.171 2148 Planarity : 0.006 0.047 2295 Dihedral : 15.321 144.959 2518 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.29 % Allowed : 11.85 % Favored : 85.86 % 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: 0.82 (0.21), residues: 1524 helix: 1.62 (0.23), residues: 482 sheet: 1.05 (0.27), residues: 376 loop : -0.54 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 22 TYR 0.020 0.002 TYR A 380 PHE 0.015 0.002 PHE A 232 TRP 0.016 0.001 TRP A 136 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (13970) covalent geometry : angle 0.58345 / 0.33 (19246) hydrogen bonds : bond 0.05536 / 3.57 ( 605) hydrogen bonds : angle 4.72435 / 3.30 ( 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 169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.442 Fit side-chains REVERT: A 91 GLU cc_start: 0.7157 (tt0) cc_final: 0.6831 (tp30) REVERT: A 94 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7836 (mm) REVERT: A 165 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8430 (tttt) REVERT: A 259 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6943 (mp0) REVERT: A 425 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: A 485 ASP cc_start: 0.7613 (m-30) cc_final: 0.7328 (m-30) REVERT: a 255 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6681 (mmm-85) REVERT: a 266 VAL cc_start: 0.7136 (t) cc_final: 0.6716 (t) REVERT: a 417 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7235 (mppt) REVERT: a 460 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6844 (mp0) outliers start: 30 outliers final: 11 residues processed: 157 average time/residue: 0.6642 time to fit residues: 111.9329 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 298 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain a residue 36 THR 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 255 ARG Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 676 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 646 GLN a 55 GLN a 449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124269 restraints weight = 14331.280| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.70 r_work: 0.3252 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13970 Z= 0.115 Angle : 0.497 7.076 19246 Z= 0.285 Chirality : 0.041 0.183 2148 Planarity : 0.005 0.041 2295 Dihedral : 15.160 142.990 2518 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.61 % Allowed : 13.61 % Favored : 84.79 % 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: 1.18 (0.21), residues: 1524 helix: 1.97 (0.23), residues: 482 sheet: 1.24 (0.27), residues: 376 loop : -0.36 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 22 TYR 0.017 0.001 TYR a 380 PHE 0.012 0.001 PHE A 232 TRP 0.013 0.001 TRP A 136 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (13970) covalent geometry : angle 0.49661 / 0.28 (19246) hydrogen bonds : bond 0.04081 / 2.62 ( 605) hydrogen bonds : angle 4.40939 / 3.05 ( 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: 21 poor density : 148 time to evaluate : 0.404 Fit side-chains REVERT: A 91 GLU cc_start: 0.7147 (tt0) cc_final: 0.6813 (tp30) REVERT: A 94 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 259 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6877 (mp0) REVERT: A 271 GLU cc_start: 0.7171 (pm20) cc_final: 0.6620 (tt0) REVERT: A 485 ASP cc_start: 0.7521 (m-30) cc_final: 0.7232 (m-30) REVERT: a 255 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6742 (mmm-85) REVERT: a 266 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6701 (t) REVERT: a 417 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7216 (mppt) REVERT: a 460 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7439 (mm-30) outliers start: 21 outliers final: 7 residues processed: 155 average time/residue: 0.6909 time to fit residues: 114.6779 Evaluate side-chains 146 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 132 SER Chi-restraints excluded: chain a residue 255 ARG Chi-restraints excluded: chain a residue 266 VAL 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 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 439 GLN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118747 restraints weight = 14362.339| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.78 r_work: 0.3174 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13970 Z= 0.213 Angle : 0.613 8.353 19246 Z= 0.338 Chirality : 0.046 0.197 2148 Planarity : 0.006 0.046 2295 Dihedral : 15.308 145.426 2518 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.76 % Allowed : 14.07 % Favored : 84.17 % 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: 0.90 (0.21), residues: 1524 helix: 1.69 (0.23), residues: 482 sheet: 1.12 (0.27), residues: 376 loop : -0.50 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 157 TYR 0.024 0.002 TYR A 380 PHE 0.017 0.002 PHE a 545 TRP 0.013 0.002 TRP A 620 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (13970) covalent geometry : angle 0.61279 / 0.34 (19246) hydrogen bonds : bond 0.05743 / 3.71 ( 605) hydrogen bonds : angle 4.67655 / 3.26 ( 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 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.389 Fit side-chains REVERT: A 91 GLU cc_start: 0.7202 (tt0) cc_final: 0.6837 (tp30) REVERT: A 94 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7789 (mm) REVERT: A 165 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8461 (tttt) REVERT: A 271 GLU cc_start: 0.7217 (pm20) cc_final: 0.6406 (tp30) REVERT: A 361 ASN cc_start: 0.8152 (m-40) cc_final: 0.7899 (t0) REVERT: A 425 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: A 485 ASP cc_start: 0.7646 (m-30) cc_final: 0.7347 (m-30) REVERT: a 94 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7854 (mm) REVERT: a 255 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6575 (mtm180) REVERT: a 266 VAL cc_start: 0.7095 (t) cc_final: 0.6828 (t) REVERT: a 417 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7277 (mppt) REVERT: a 460 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6838 (mp0) outliers start: 23 outliers final: 8 residues processed: 151 average time/residue: 0.6958 time to fit residues: 112.6441 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 298 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain a residue 65 TRP Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 255 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3737 r_free = 0.3737 target = 0.152145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122833 restraints weight = 14209.857| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.72 r_work: 0.3231 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13970 Z= 0.123 Angle : 0.517 7.306 19246 Z= 0.294 Chirality : 0.042 0.176 2148 Planarity : 0.005 0.043 2295 Dihedral : 15.180 143.550 2518 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.30 % Allowed : 14.83 % Favored : 83.87 % 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: 1.10 (0.21), residues: 1524 helix: 1.94 (0.24), residues: 480 sheet: 1.20 (0.27), residues: 376 loop : -0.43 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 157 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 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13970) covalent geometry : angle 0.51716 / 0.29 (19246) hydrogen bonds : bond 0.04358 / 2.79 ( 605) hydrogen bonds : angle 4.43394 / 3.08 ( 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 163 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.480 Fit side-chains REVERT: A 91 GLU cc_start: 0.7141 (tt0) cc_final: 0.6783 (tp30) REVERT: A 94 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7789 (mm) REVERT: A 271 GLU cc_start: 0.7182 (pm20) cc_final: 0.6619 (tt0) REVERT: A 361 ASN cc_start: 0.8134 (m-40) cc_final: 0.7895 (t0) REVERT: A 485 ASP cc_start: 0.7554 (m-30) cc_final: 0.7269 (m-30) REVERT: a 94 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7767 (mm) REVERT: a 99 GLU cc_start: 0.7628 (tp30) cc_final: 0.7184 (tp30) REVERT: a 126 ASP cc_start: 0.8540 (m-30) cc_final: 0.7872 (m-30) REVERT: a 255 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6617 (mtm180) REVERT: a 266 VAL cc_start: 0.7079 (t) cc_final: 0.6812 (t) REVERT: a 417 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7240 (mppt) REVERT: a 460 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7376 (mm-30) outliers start: 17 outliers final: 6 residues processed: 153 average time/residue: 0.7116 time to fit residues: 116.8753 Evaluate side-chains 149 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 94 ILE 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 417 LYS Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 687 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN a 55 GLN a 449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122062 restraints weight = 14413.491| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.71 r_work: 0.3222 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1520 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= 0.124 Angle : 0.514 7.215 19246 Z= 0.291 Chirality : 0.042 0.170 2148 Planarity : 0.005 0.068 2295 Dihedral : 15.112 143.290 2518 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.38 % Allowed : 15.14 % Favored : 83.49 % 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: 1.20 (0.21), residues: 1524 helix: 2.03 (0.24), residues: 480 sheet: 1.24 (0.28), residues: 376 loop : -0.38 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 419 TYR 0.017 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 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (13970) covalent geometry : angle 0.51364 / 0.29 (19246) hydrogen bonds : bond 0.04219 / 2.70 ( 605) hydrogen bonds : angle 4.36290 / 3.03 ( 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 161 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.474 Fit side-chains REVERT: A 91 GLU cc_start: 0.7113 (tt0) cc_final: 0.6792 (tp30) REVERT: A 94 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7783 (mm) REVERT: A 256 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7058 (pt0) REVERT: A 271 GLU cc_start: 0.7170 (pm20) cc_final: 0.6607 (tt0) REVERT: A 361 ASN cc_start: 0.8153 (m-40) cc_final: 0.7909 (t0) REVERT: A 485 ASP cc_start: 0.7566 (m-30) cc_final: 0.7265 (m-30) REVERT: a 94 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7856 (mm) REVERT: a 99 GLU cc_start: 0.7609 (tp30) cc_final: 0.7182 (tp30) REVERT: a 126 ASP cc_start: 0.8544 (m-30) cc_final: 0.7846 (m-30) REVERT: a 255 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6612 (mtm180) REVERT: a 266 VAL cc_start: 0.7057 (t) cc_final: 0.6772 (t) REVERT: a 417 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7291 (mppt) REVERT: a 460 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7373 (mm-30) outliers start: 18 outliers final: 8 residues processed: 149 average time/residue: 0.7563 time to fit residues: 120.7848 Evaluate side-chains 156 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 259 GLU Chi-restraints excluded: chain A residue 298 GLU 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 255 ARG 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 148 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116887 restraints weight = 14387.856| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.68 r_work: 0.3144 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13970 Z= 0.251 Angle : 0.661 9.264 19246 Z= 0.361 Chirality : 0.048 0.221 2148 Planarity : 0.006 0.077 2295 Dihedral : 15.410 145.974 2518 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.30 % Allowed : 15.52 % 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: 0.77 (0.21), residues: 1524 helix: 1.59 (0.23), residues: 480 sheet: 1.04 (0.27), residues: 376 loop : -0.59 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG a 419 TYR 0.027 0.002 TYR A 380 PHE 0.018 0.002 PHE a 545 TRP 0.013 0.002 TRP A 136 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (13970) covalent geometry : angle 0.66079 / 0.36 (19246) hydrogen bonds : bond 0.06239 / 4.03 ( 605) hydrogen bonds : angle 4.73868 / 3.32 ( 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: 17 poor density : 143 time to evaluate : 0.412 Fit side-chains REVERT: A 91 GLU cc_start: 0.7144 (tt0) cc_final: 0.6801 (tp30) REVERT: A 94 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7769 (mm) REVERT: A 271 GLU cc_start: 0.7284 (pm20) cc_final: 0.6431 (tp30) REVERT: A 361 ASN cc_start: 0.8166 (m-40) cc_final: 0.7893 (t0) REVERT: A 485 ASP cc_start: 0.7674 (m-30) cc_final: 0.7367 (m-30) REVERT: a 94 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7821 (mm) REVERT: a 99 GLU cc_start: 0.7700 (tp30) cc_final: 0.7271 (tp30) REVERT: a 255 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6582 (mtm180) REVERT: a 266 VAL cc_start: 0.7105 (t) cc_final: 0.6819 (t) REVERT: a 417 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7312 (mppt) REVERT: a 460 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6805 (mp0) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.7263 time to fit residues: 116.2093 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 259 GLU Chi-restraints excluded: chain A residue 432 VAL 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 255 ARG Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain a residue 428 GLU Chi-restraints excluded: chain a residue 460 GLU Chi-restraints excluded: chain a residue 687 GLU Chi-restraints excluded: chain a residue 701 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3716 r_free = 0.3716 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121577 restraints weight = 14388.825| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.71 r_work: 0.3213 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1542 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 : 0.526 7.242 19246 Z= 0.299 Chirality : 0.042 0.181 2148 Planarity : 0.005 0.064 2295 Dihedral : 15.216 143.553 2518 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.38 % Allowed : 15.52 % Favored : 83.10 % 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: 1.04 (0.21), residues: 1524 helix: 1.89 (0.24), residues: 480 sheet: 1.17 (0.27), residues: 376 loop : -0.46 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG a 419 TYR 0.017 0.001 TYR A 380 PHE 0.013 0.001 PHE A 232 TRP 0.014 0.001 TRP A 136 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (13970) covalent geometry : angle 0.52595 / 0.30 (19246) hydrogen bonds : bond 0.04395 / 2.81 ( 605) hydrogen bonds : angle 4.41902 / 3.08 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4210.06 seconds wall clock time: 72 minutes 22.53 seconds (4342.53 seconds total)