Starting phenix.real_space_refine on Sat Aug 8 21:43:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.cif" model { file = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b4h_15848/08_2026/8b4h_15848.map" } resolution = 3.35 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= 0.004 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: 7 Type Number sf(0) Gaussians P 224 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 9898 2.51 5 N 2892 2.21 5 O 3498 1.98 5 H 14570 0.53 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31138 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 5967 Classifications: {'peptide': 358} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain: "B" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 5967 Classifications: {'peptide': 358} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain: "C" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 6043 Classifications: {'peptide': 362} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 1 Chain: "D" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 6043 Classifications: {'peptide': 362} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 1 Chain: "E" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1803 Classifications: {'DNA': 57} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 56} Chain: "F" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1755 Classifications: {'DNA': 55} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 54} Chain: "G" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1803 Classifications: {'DNA': 57} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 56} Chain: "H" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1755 Classifications: {'DNA': 55} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 54} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.95, per 1000 atoms: 0.16 Number of scatterers: 31138 At special positions: 0 Unit cell: (94.34, 102.82, 218.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 54 16.00 P 224 15.00 Mg 2 11.99 O 3498 8.00 N 2892 7.00 C 9898 6.00 H 14570 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 785.0 milliseconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 42.5% alpha, 14.3% beta 50 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.795A pdb=" N HIS A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.610A pdb=" N GLN A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 104 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 204 through 215 Processing helix chain 'A' and resid 225 through 228 removed outlier: 3.699A pdb=" N THR A 228 " --> pdb=" O ARG A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.795A pdb=" N HIS B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.610A pdb=" N GLN B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 104 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 225 through 228 removed outlier: 3.699A pdb=" N THR B 228 " --> pdb=" O ARG B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 251 through 266 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.695A pdb=" N HIS C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 91 through 108 Proline residue: C 100 - end of helix removed outlier: 3.549A pdb=" N LYS C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.565A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 285 removed outlier: 3.736A pdb=" N ARG C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 360 through 373 removed outlier: 3.507A pdb=" N LYS C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 30 through 39 removed outlier: 3.695A pdb=" N HIS D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 91 through 108 Proline residue: D 100 - end of helix removed outlier: 3.549A pdb=" N LYS D 108 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 235 through 243 Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.565A pdb=" N ALA D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.736A pdb=" N ARG D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 360 through 373 removed outlier: 3.507A pdb=" N LYS D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 373 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 158 removed outlier: 5.789A pdb=" N LYS A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 132 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 138 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU A 130 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 140 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 305 removed outlier: 4.693A pdb=" N LEU A 342 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.550A pdb=" N GLN A 318 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 158 removed outlier: 5.789A pdb=" N LYS B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 132 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 138 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 130 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 140 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 303 through 305 removed outlier: 4.693A pdb=" N LEU B 342 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.550A pdb=" N GLN B 318 " --> pdb=" O GLN B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 153 through 158 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'C' and resid 193 through 196 removed outlier: 5.470A pdb=" N LYS C 202 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AB2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AB3, first strand: chain 'D' and resid 153 through 158 Processing sheet with id=AB4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AB5, first strand: chain 'D' and resid 193 through 196 removed outlier: 5.469A pdb=" N LYS D 202 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB7, first strand: chain 'D' and resid 311 through 314 506 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 7.10 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14562 1.03 - 1.23: 82 1.23 - 1.42: 7616 1.42 - 1.62: 9616 1.62 - 1.81: 100 Bond restraints: 31976 Sorted by residual: bond pdb=" C3' DC F 49 " pdb=" O3' DC F 49 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C3' DC H 49 " pdb=" O3' DC H 49 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C3' DC E 9 " pdb=" C2' DC E 9 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DC G 9 " pdb=" C2' DC G 9 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DT H 50 " pdb=" O3' DT H 50 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.25e+01 ... (remaining 31971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 52909 1.31 - 2.62: 4459 2.62 - 3.93: 458 3.93 - 5.24: 22 5.24 - 6.55: 10 Bond angle restraints: 57858 Sorted by residual: angle pdb=" O5' DT E 8 " pdb=" C5' DT E 8 " pdb=" C4' DT E 8 " ideal model delta sigma weight residual 109.40 113.26 -3.86 8.00e-01 1.56e+00 2.32e+01 angle pdb=" O5' DT G 8 " pdb=" C5' DT G 8 " pdb=" C4' DT G 8 " ideal model delta sigma weight residual 109.40 113.26 -3.86 8.00e-01 1.56e+00 2.32e+01 angle pdb=" O4' DT G 8 " pdb=" C1' DT G 8 " pdb=" N1 DT G 8 " ideal model delta sigma weight residual 108.00 111.04 -3.04 7.00e-01 2.04e+00 1.89e+01 angle pdb=" O4' DT E 8 " pdb=" C1' DT E 8 " pdb=" N1 DT E 8 " ideal model delta sigma weight residual 108.00 111.04 -3.04 7.00e-01 2.04e+00 1.89e+01 angle pdb=" N3 DT H 50 " pdb=" C4 DT H 50 " pdb=" O4 DT H 50 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 57853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 11111 16.02 - 32.04: 1399 32.04 - 48.07: 1065 48.07 - 64.09: 589 64.09 - 80.11: 8 Dihedral angle restraints: 14172 sinusoidal: 9010 harmonic: 5162 Sorted by residual: dihedral pdb=" CA LYS C 32 " pdb=" C LYS C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS D 32 " pdb=" C LYS D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CB GLU B 253 " pdb=" CG GLU B 253 " pdb=" CD GLU B 253 " pdb=" OE1 GLU B 253 " ideal model delta sinusoidal sigma weight residual 0.00 -80.11 80.11 1 3.00e+01 1.11e-03 8.83e+00 ... (remaining 14169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1523 0.031 - 0.062: 646 0.062 - 0.093: 243 0.093 - 0.124: 136 0.124 - 0.155: 32 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C1' DG H 8 " pdb=" O4' DG H 8 " pdb=" C2' DG H 8 " pdb=" N9 DG H 8 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" C1' DG F 8 " pdb=" O4' DG F 8 " pdb=" C2' DG F 8 " pdb=" N9 DG F 8 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" C3' DA H 55 " pdb=" C4' DA H 55 " pdb=" O3' DA H 55 " pdb=" C2' DA H 55 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 2577 not shown) Planarity restraints: 3846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC E 52 " -0.034 2.00e-02 2.50e+03 2.94e-02 2.37e+01 pdb=" N1 DC E 52 " 0.079 2.00e-02 2.50e+03 pdb=" C2 DC E 52 " -0.044 2.00e-02 2.50e+03 pdb=" O2 DC E 52 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC E 52 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC E 52 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC E 52 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DC E 52 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC E 52 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC E 52 " -0.006 2.00e-02 2.50e+03 pdb=" H6 DC E 52 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC G 52 " 0.034 2.00e-02 2.50e+03 2.94e-02 2.37e+01 pdb=" N1 DC G 52 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DC G 52 " 0.044 2.00e-02 2.50e+03 pdb=" O2 DC G 52 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC G 52 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC G 52 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC G 52 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC G 52 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC G 52 " 0.001 2.00e-02 2.50e+03 pdb=" H5 DC G 52 " 0.006 2.00e-02 2.50e+03 pdb=" H6 DC G 52 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC E 53 " -0.029 2.00e-02 2.50e+03 2.15e-02 1.27e+01 pdb=" N1 DC E 53 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC E 53 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC E 53 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC E 53 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC E 53 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC E 53 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC E 53 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC E 53 " 0.004 2.00e-02 2.50e+03 pdb=" H5 DC E 53 " -0.007 2.00e-02 2.50e+03 pdb=" H6 DC E 53 " -0.004 2.00e-02 2.50e+03 ... (remaining 3843 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 764 2.12 - 2.74: 53137 2.74 - 3.36: 83110 3.36 - 3.98: 111902 3.98 - 4.60: 173717 Nonbonded interactions: 422630 Sorted by model distance: nonbonded pdb=" H GLY B 90 " pdb=" OP2 DC F 45 " model vdw 1.502 2.450 nonbonded pdb=" H GLY A 90 " pdb=" OP2 DC H 45 " model vdw 1.502 2.450 nonbonded pdb="HH22 ARG C 52 " pdb=" O2 DT E 44 " model vdw 1.514 2.450 nonbonded pdb="HH22 ARG D 52 " pdb=" O2 DT G 44 " model vdw 1.515 2.450 nonbonded pdb=" HZ2 LYS D 32 " pdb=" O6 DG H 8 " model vdw 1.553 2.450 ... (remaining 422625 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.210 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 30.780 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.006 0.049 17406 Z= 0.454 Angle : 0.778 6.553 24374 Z= 0.662 Chirality : 0.045 0.155 2580 Planarity : 0.006 0.093 2308 Dihedral : 22.551 80.111 7224 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.23), residues: 1428 helix: 1.34 (0.22), residues: 550 sheet: -1.97 (0.32), residues: 194 loop : -0.85 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 4 TYR 0.013 0.001 TYR B 214 PHE 0.024 0.001 PHE B 257 TRP 0.007 0.001 TRP B 262 HIS 0.009 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.45 (17406) covalent geometry : angle 0.77833 / 0.66 (24374) hydrogen bonds : bond 0.11138 / 7.16 ( 630) hydrogen bonds : angle 5.22142 / 3.65 ( 1676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 LEU cc_start: 0.8239 (tt) cc_final: 0.7965 (tp) REVERT: D 291 LEU cc_start: 0.8241 (tt) cc_final: 0.7966 (tp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2262 time to fit residues: 57.5946 Evaluate side-chains 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.218923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177629 restraints weight = 58247.265| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.30 r_work: 0.3863 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17406 Z= 0.201 Angle : 0.755 7.994 24374 Z= 0.419 Chirality : 0.046 0.203 2580 Planarity : 0.006 0.099 2308 Dihedral : 27.359 70.179 4094 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.46 % Allowed : 3.02 % Favored : 96.52 % 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: -0.62 (0.22), residues: 1428 helix: 0.88 (0.21), residues: 548 sheet: -2.09 (0.32), residues: 194 loop : -0.90 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 102 TYR 0.009 0.001 TYR A 214 PHE 0.014 0.002 PHE A 257 TRP 0.010 0.001 TRP C 125 HIS 0.005 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (17406) covalent geometry : angle 0.75477 / 0.42 (24374) hydrogen bonds : bond 0.05431 / 3.49 ( 630) hydrogen bonds : angle 4.61760 / 3.21 ( 1676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 264 ASP cc_start: 0.7881 (t0) cc_final: 0.7632 (t0) REVERT: D 264 ASP cc_start: 0.7835 (t0) cc_final: 0.7515 (t0) outliers start: 6 outliers final: 6 residues processed: 154 average time/residue: 0.2433 time to fit residues: 57.6672 Evaluate side-chains 135 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN C 265 GLN D 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.216245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174653 restraints weight = 57677.429| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.27 r_work: 0.3834 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17406 Z= 0.167 Angle : 0.636 5.989 24374 Z= 0.368 Chirality : 0.042 0.205 2580 Planarity : 0.004 0.070 2308 Dihedral : 27.422 62.764 4094 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.62 % Allowed : 4.72 % Favored : 94.66 % 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: -0.61 (0.22), residues: 1428 helix: 0.87 (0.21), residues: 554 sheet: -2.09 (0.31), residues: 194 loop : -0.89 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.021 0.001 TYR C 87 PHE 0.014 0.002 PHE A 216 TRP 0.010 0.001 TRP D 125 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (17406) covalent geometry : angle 0.63564 / 0.37 (24374) hydrogen bonds : bond 0.04500 / 2.90 ( 630) hydrogen bonds : angle 4.42565 / 3.09 ( 1676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: A 152 MET cc_start: 0.8133 (tpt) cc_final: 0.7323 (tpt) REVERT: A 219 LYS cc_start: 0.7012 (tptt) cc_final: 0.6781 (tptt) REVERT: B 69 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: B 114 GLU cc_start: 0.6636 (pp20) cc_final: 0.6391 (pp20) REVERT: B 152 MET cc_start: 0.8130 (tpt) cc_final: 0.7320 (tpt) REVERT: B 219 LYS cc_start: 0.7004 (tptt) cc_final: 0.6774 (tptt) REVERT: C 264 ASP cc_start: 0.7979 (t0) cc_final: 0.7753 (t0) REVERT: C 291 LEU cc_start: 0.8515 (tt) cc_final: 0.8210 (tp) REVERT: D 264 ASP cc_start: 0.7897 (t0) cc_final: 0.7672 (t0) REVERT: D 291 LEU cc_start: 0.8511 (tt) cc_final: 0.8206 (tp) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 0.2622 time to fit residues: 57.6682 Evaluate side-chains 134 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 71 optimal weight: 20.0000 chunk 74 optimal weight: 0.0470 chunk 160 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.218044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175635 restraints weight = 57389.377| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.38 r_work: 0.3852 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17406 Z= 0.120 Angle : 0.581 5.415 24374 Z= 0.331 Chirality : 0.040 0.201 2580 Planarity : 0.004 0.068 2308 Dihedral : 27.354 63.067 4094 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.54 % Allowed : 5.19 % Favored : 94.27 % 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: -0.25 (0.22), residues: 1428 helix: 1.24 (0.22), residues: 552 sheet: -1.94 (0.32), residues: 194 loop : -0.75 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 282 TYR 0.014 0.001 TYR A 214 PHE 0.027 0.001 PHE C 157 TRP 0.008 0.001 TRP A 125 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (17406) covalent geometry : angle 0.58061 / 0.33 (24374) hydrogen bonds : bond 0.03775 / 2.45 ( 630) hydrogen bonds : angle 4.10865 / 2.87 ( 1676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: A 114 GLU cc_start: 0.6260 (pp20) cc_final: 0.6012 (pp20) REVERT: A 152 MET cc_start: 0.8089 (tpt) cc_final: 0.7301 (tpt) REVERT: A 219 LYS cc_start: 0.7061 (tptt) cc_final: 0.6851 (tptt) REVERT: B 69 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: B 114 GLU cc_start: 0.6553 (pp20) cc_final: 0.6317 (pp20) REVERT: B 152 MET cc_start: 0.8080 (tpt) cc_final: 0.7289 (tpt) REVERT: B 219 LYS cc_start: 0.7055 (tptt) cc_final: 0.6849 (tptt) REVERT: D 264 ASP cc_start: 0.7936 (t0) cc_final: 0.7717 (t0) outliers start: 7 outliers final: 5 residues processed: 140 average time/residue: 0.2424 time to fit residues: 52.3379 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 265 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.209862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.166975 restraints weight = 57781.357| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.55 r_work: 0.3714 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17406 Z= 0.271 Angle : 0.697 8.199 24374 Z= 0.385 Chirality : 0.046 0.235 2580 Planarity : 0.005 0.074 2308 Dihedral : 27.315 72.033 4094 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.08 % Allowed : 6.42 % Favored : 92.49 % 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: -0.90 (0.22), residues: 1428 helix: 0.57 (0.21), residues: 554 sheet: -2.26 (0.31), residues: 196 loop : -0.98 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 4 TYR 0.018 0.002 TYR B 238 PHE 0.021 0.002 PHE B 79 TRP 0.018 0.002 TRP C 125 HIS 0.004 0.001 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.27 (17406) covalent geometry : angle 0.69730 / 0.38 (24374) hydrogen bonds : bond 0.04979 / 3.26 ( 630) hydrogen bonds : angle 4.63154 / 3.23 ( 1676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7617 (m-30) cc_final: 0.7393 (m-30) REVERT: A 114 GLU cc_start: 0.6350 (pp20) cc_final: 0.6035 (pp20) REVERT: B 96 ASP cc_start: 0.7617 (m-30) cc_final: 0.7402 (m-30) REVERT: C 160 SER cc_start: 0.8131 (t) cc_final: 0.7779 (m) REVERT: C 291 LEU cc_start: 0.8523 (tt) cc_final: 0.8213 (tp) REVERT: D 160 SER cc_start: 0.8167 (t) cc_final: 0.7801 (m) REVERT: D 291 LEU cc_start: 0.8527 (tt) cc_final: 0.8216 (tp) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.2441 time to fit residues: 51.6662 Evaluate side-chains 132 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.213622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171536 restraints weight = 57420.540| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.53 r_work: 0.3771 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17406 Z= 0.123 Angle : 0.574 8.050 24374 Z= 0.327 Chirality : 0.040 0.181 2580 Planarity : 0.004 0.077 2308 Dihedral : 27.265 68.372 4094 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.24 % Allowed : 7.20 % Favored : 91.56 % 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: -0.56 (0.22), residues: 1428 helix: 0.96 (0.22), residues: 556 sheet: -2.17 (0.31), residues: 194 loop : -0.89 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.013 0.001 TYR B 214 PHE 0.013 0.001 PHE A 210 TRP 0.009 0.001 TRP D 308 HIS 0.003 0.001 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (17406) covalent geometry : angle 0.57360 / 0.33 (24374) hydrogen bonds : bond 0.03637 / 2.36 ( 630) hydrogen bonds : angle 4.19777 / 2.93 ( 1676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: A 96 ASP cc_start: 0.7513 (m-30) cc_final: 0.7239 (m-30) REVERT: A 114 GLU cc_start: 0.6467 (pp20) cc_final: 0.6187 (pp20) REVERT: A 152 MET cc_start: 0.8233 (tpt) cc_final: 0.7399 (tpt) REVERT: A 171 ILE cc_start: 0.7301 (mm) cc_final: 0.7033 (mt) REVERT: B 69 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: B 96 ASP cc_start: 0.7513 (m-30) cc_final: 0.7243 (m-30) REVERT: B 152 MET cc_start: 0.8237 (tpt) cc_final: 0.7396 (tpt) REVERT: B 171 ILE cc_start: 0.7282 (mm) cc_final: 0.7016 (mt) REVERT: C 264 ASP cc_start: 0.8101 (t0) cc_final: 0.7881 (t0) REVERT: C 291 LEU cc_start: 0.8551 (tt) cc_final: 0.8202 (tp) REVERT: D 264 ASP cc_start: 0.8037 (t0) cc_final: 0.7815 (t0) REVERT: D 291 LEU cc_start: 0.8552 (tt) cc_final: 0.8206 (tp) outliers start: 16 outliers final: 8 residues processed: 135 average time/residue: 0.2366 time to fit residues: 49.5492 Evaluate side-chains 132 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 157 optimal weight: 40.0000 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.214559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173746 restraints weight = 57675.944| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.29 r_work: 0.3770 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17406 Z= 0.153 Angle : 0.578 6.309 24374 Z= 0.328 Chirality : 0.041 0.188 2580 Planarity : 0.004 0.064 2308 Dihedral : 27.056 70.727 4094 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.24 % Allowed : 7.74 % Favored : 91.02 % 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: -0.50 (0.22), residues: 1428 helix: 1.06 (0.22), residues: 556 sheet: -2.10 (0.31), residues: 198 loop : -0.89 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 282 TYR 0.025 0.001 TYR D 87 PHE 0.012 0.001 PHE D 207 TRP 0.009 0.001 TRP D 125 HIS 0.004 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (17406) covalent geometry : angle 0.57764 / 0.33 (24374) hydrogen bonds : bond 0.03608 / 2.35 ( 630) hydrogen bonds : angle 4.18440 / 2.93 ( 1676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7634 (m-30) cc_final: 0.7379 (m-30) REVERT: A 114 GLU cc_start: 0.6453 (pp20) cc_final: 0.6187 (pp20) REVERT: A 152 MET cc_start: 0.8203 (tpt) cc_final: 0.7413 (tpt) REVERT: A 171 ILE cc_start: 0.7339 (mm) cc_final: 0.6946 (mt) REVERT: B 96 ASP cc_start: 0.7650 (m-30) cc_final: 0.7399 (m-30) REVERT: B 152 MET cc_start: 0.8206 (tpt) cc_final: 0.7411 (tpt) REVERT: B 171 ILE cc_start: 0.7325 (mm) cc_final: 0.6935 (mt) REVERT: C 264 ASP cc_start: 0.8036 (t0) cc_final: 0.7787 (t0) REVERT: C 291 LEU cc_start: 0.8546 (tt) cc_final: 0.8186 (tp) REVERT: D 264 ASP cc_start: 0.8046 (t0) cc_final: 0.7813 (t0) REVERT: D 291 LEU cc_start: 0.8546 (tt) cc_final: 0.8188 (tp) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.2156 time to fit residues: 44.6750 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.168717 restraints weight = 58824.555| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.40 r_work: 0.3746 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17406 Z= 0.126 Angle : 0.550 6.035 24374 Z= 0.315 Chirality : 0.040 0.176 2580 Planarity : 0.004 0.064 2308 Dihedral : 27.008 71.217 4094 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.16 % Allowed : 7.74 % Favored : 91.10 % 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: -0.44 (0.22), residues: 1428 helix: 1.18 (0.22), residues: 556 sheet: -2.17 (0.32), residues: 178 loop : -0.96 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 261 TYR 0.018 0.001 TYR D 87 PHE 0.012 0.001 PHE D 157 TRP 0.008 0.001 TRP A 125 HIS 0.002 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (17406) covalent geometry : angle 0.55008 / 0.31 (24374) hydrogen bonds : bond 0.03337 / 2.18 ( 630) hydrogen bonds : angle 4.07173 / 2.85 ( 1676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7508 (m-30) cc_final: 0.7154 (m-30) REVERT: A 114 GLU cc_start: 0.6281 (pp20) cc_final: 0.6031 (pp20) REVERT: A 152 MET cc_start: 0.8039 (tpt) cc_final: 0.7219 (tpt) REVERT: B 96 ASP cc_start: 0.7517 (m-30) cc_final: 0.7160 (m-30) REVERT: B 152 MET cc_start: 0.8030 (tpt) cc_final: 0.7206 (tpt) REVERT: C 212 SER cc_start: 0.7604 (m) cc_final: 0.7202 (p) REVERT: C 291 LEU cc_start: 0.8515 (tt) cc_final: 0.8179 (tp) REVERT: D 212 SER cc_start: 0.7618 (m) cc_final: 0.7222 (p) REVERT: D 291 LEU cc_start: 0.8517 (tt) cc_final: 0.8180 (tp) outliers start: 15 outliers final: 14 residues processed: 138 average time/residue: 0.2337 time to fit residues: 49.5737 Evaluate side-chains 140 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 147 optimal weight: 40.0000 chunk 70 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.207091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.163599 restraints weight = 58431.931| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.60 r_work: 0.3681 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17406 Z= 0.210 Angle : 0.616 6.713 24374 Z= 0.345 Chirality : 0.043 0.215 2580 Planarity : 0.005 0.062 2308 Dihedral : 26.947 75.513 4094 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.16 % Allowed : 8.13 % Favored : 90.71 % 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 (0.22), residues: 1428 helix: 0.84 (0.22), residues: 556 sheet: -2.22 (0.33), residues: 176 loop : -1.09 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 4 TYR 0.017 0.002 TYR A 238 PHE 0.020 0.002 PHE B 79 TRP 0.012 0.002 TRP C 125 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (17406) covalent geometry : angle 0.61622 / 0.35 (24374) hydrogen bonds : bond 0.04051 / 2.67 ( 630) hydrogen bonds : angle 4.36439 / 3.06 ( 1676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7678 (m-30) cc_final: 0.7425 (m-30) REVERT: A 114 GLU cc_start: 0.6434 (pp20) cc_final: 0.6213 (pp20) REVERT: A 152 MET cc_start: 0.8101 (tpt) cc_final: 0.7255 (tpt) REVERT: B 96 ASP cc_start: 0.7674 (m-30) cc_final: 0.7415 (m-30) REVERT: B 152 MET cc_start: 0.8103 (tpt) cc_final: 0.7256 (tpt) outliers start: 15 outliers final: 14 residues processed: 133 average time/residue: 0.2497 time to fit residues: 51.4057 Evaluate side-chains 135 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 158 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 131 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.207875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164773 restraints weight = 58307.225| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.58 r_work: 0.3693 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17406 Z= 0.159 Angle : 0.575 6.601 24374 Z= 0.328 Chirality : 0.041 0.199 2580 Planarity : 0.004 0.063 2308 Dihedral : 26.896 73.995 4094 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.16 % Allowed : 8.44 % Favored : 90.40 % 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: -0.70 (0.22), residues: 1428 helix: 0.96 (0.22), residues: 556 sheet: -2.25 (0.33), residues: 176 loop : -1.12 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 261 TYR 0.032 0.001 TYR C 87 PHE 0.016 0.002 PHE C 157 TRP 0.010 0.001 TRP C 125 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (17406) covalent geometry : angle 0.57522 / 0.33 (24374) hydrogen bonds : bond 0.03593 / 2.37 ( 630) hydrogen bonds : angle 4.25424 / 2.99 ( 1676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7590 (m-30) cc_final: 0.7336 (m-30) REVERT: A 114 GLU cc_start: 0.6373 (pp20) cc_final: 0.6146 (pp20) REVERT: A 152 MET cc_start: 0.8036 (tpt) cc_final: 0.7212 (tpt) REVERT: B 96 ASP cc_start: 0.7592 (m-30) cc_final: 0.7336 (m-30) REVERT: B 152 MET cc_start: 0.8051 (tpt) cc_final: 0.7227 (tpt) REVERT: C 297 ASP cc_start: 0.7358 (t0) cc_final: 0.7099 (p0) REVERT: D 297 ASP cc_start: 0.7372 (t0) cc_final: 0.7103 (p0) outliers start: 15 outliers final: 14 residues processed: 136 average time/residue: 0.2492 time to fit residues: 52.0393 Evaluate side-chains 139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.209412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166301 restraints weight = 58735.871| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.64 r_work: 0.3732 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17406 Z= 0.122 Angle : 0.547 6.516 24374 Z= 0.315 Chirality : 0.040 0.181 2580 Planarity : 0.004 0.059 2308 Dihedral : 26.792 75.271 4094 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.93 % Allowed : 8.51 % Favored : 90.56 % 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: -0.46 (0.22), residues: 1428 helix: 1.20 (0.22), residues: 556 sheet: -2.08 (0.33), residues: 176 loop : -1.03 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 261 TYR 0.013 0.001 TYR A 238 PHE 0.015 0.001 PHE D 157 TRP 0.008 0.001 TRP B 125 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (17406) covalent geometry : angle 0.54681 / 0.31 (24374) hydrogen bonds : bond 0.03249 / 2.14 ( 630) hydrogen bonds : angle 4.07081 / 2.86 ( 1676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6504.83 seconds wall clock time: 111 minutes 0.83 seconds (6660.83 seconds total)