Starting phenix.real_space_refine on Sun Jul 5 21:55:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b4h_15848/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.map" model { file = "/net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b4h_15848/07_2026/8b4h_15848.cif" } 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-dev-6108/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: 4.41, per 1000 atoms: 0.14 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: 2.79 Conformation dependent library (CDL) restraints added in 776.0 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: 5.12 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: 3.94 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: 52929 1.31 - 2.62: 4447 2.62 - 3.93: 450 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: 0.04 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: 1.930 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: 0.180 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 31.460 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.560 ------------------------------------------------------------------------------- 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= 0.453 Angle : 0.773 6.553 24374 Z= 0.656 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 0.77280 / 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 : 0.726 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: 0.2690 time to fit residues: 68.1173 Evaluate side-chains 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN C 265 GLN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.219305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.177858 restraints weight = 58343.214| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.28 r_work: 0.3873 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17406 Z= 0.202 Angle : 0.725 7.902 24374 Z= 0.411 Chirality : 0.046 0.203 2580 Planarity : 0.005 0.083 2308 Dihedral : 27.402 69.268 4094 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.62 % Allowed : 2.86 % 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: -0.57 (0.22), residues: 1428 helix: 0.95 (0.22), residues: 546 sheet: -2.09 (0.32), residues: 194 loop : -0.88 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 4 TYR 0.008 0.001 TYR D 37 PHE 0.015 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 0.00406 / 0.20 (17406) covalent geometry : angle 0.72547 / 0.41 (24374) hydrogen bonds : bond 0.05358 / 3.43 ( 630) hydrogen bonds : angle 4.60507 / 3.20 ( 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 156 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.479 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: C 264 ASP cc_start: 0.7891 (t0) cc_final: 0.7654 (t0) REVERT: D 264 ASP cc_start: 0.7824 (t0) cc_final: 0.7515 (t0) outliers start: 8 outliers final: 6 residues processed: 154 average time/residue: 0.2485 time to fit residues: 58.4576 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.218535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176898 restraints weight = 57862.446| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.31 r_work: 0.3864 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17406 Z= 0.148 Angle : 0.616 6.172 24374 Z= 0.361 Chirality : 0.041 0.181 2580 Planarity : 0.004 0.070 2308 Dihedral : 27.414 62.164 4094 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.62 % Allowed : 3.79 % Favored : 95.59 % 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: 1.04 (0.21), residues: 550 sheet: -1.99 (0.32), residues: 194 loop : -0.82 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.021 0.001 TYR D 87 PHE 0.014 0.001 PHE B 257 TRP 0.008 0.001 TRP B 125 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (17406) covalent geometry : angle 0.61626 / 0.36 (24374) hydrogen bonds : bond 0.04401 / 2.81 ( 630) hydrogen bonds : angle 4.33365 / 3.02 ( 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 150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.763 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: 0.7153 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: A 152 MET cc_start: 0.8127 (tpt) cc_final: 0.7321 (tpt) REVERT: B 69 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: B 152 MET cc_start: 0.8120 (tpt) cc_final: 0.7315 (tpt) REVERT: C 291 LEU cc_start: 0.8513 (tt) cc_final: 0.8201 (tp) REVERT: C 317 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7418 (mt-10) REVERT: D 264 ASP cc_start: 0.7870 (t0) cc_final: 0.7573 (t0) REVERT: D 291 LEU cc_start: 0.8487 (tt) cc_final: 0.8178 (tp) REVERT: D 317 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7399 (mt-10) outliers start: 8 outliers final: 4 residues processed: 148 average time/residue: 0.2513 time to fit residues: 56.7470 Evaluate side-chains 138 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 1.9990 chunk 137 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.216983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.175357 restraints weight = 57369.349| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.29 r_work: 0.3846 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1762 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= 0.151 Angle : 0.594 5.419 24374 Z= 0.342 Chirality : 0.040 0.182 2580 Planarity : 0.004 0.068 2308 Dihedral : 27.438 65.264 4094 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.93 % Allowed : 5.42 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1428 helix: 1.08 (0.21), residues: 552 sheet: -2.02 (0.31), residues: 198 loop : -0.80 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.016 0.001 TYR C 87 PHE 0.010 0.001 PHE D 157 TRP 0.009 0.001 TRP B 125 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (17406) covalent geometry : angle 0.59405 / 0.34 (24374) hydrogen bonds : bond 0.04045 / 2.61 ( 630) hydrogen bonds : angle 4.21570 / 2.94 ( 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 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8104 (tpt) cc_final: 0.7306 (tpt) REVERT: A 219 LYS cc_start: 0.7043 (tptt) cc_final: 0.6819 (tptt) REVERT: B 152 MET cc_start: 0.8106 (tpt) cc_final: 0.7306 (tpt) REVERT: B 219 LYS cc_start: 0.7042 (tptt) cc_final: 0.6816 (tptt) REVERT: C 264 ASP cc_start: 0.7931 (t0) cc_final: 0.7638 (t0) REVERT: D 264 ASP cc_start: 0.7861 (t0) cc_final: 0.7635 (t0) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.2437 time to fit residues: 52.3304 Evaluate side-chains 136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 D residue 189 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.207121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163598 restraints weight = 57836.456| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.36 r_work: 0.3684 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 17406 Z= 0.339 Angle : 0.772 9.775 24374 Z= 0.426 Chirality : 0.050 0.271 2580 Planarity : 0.006 0.086 2308 Dihedral : 27.468 75.047 4094 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.24 % Allowed : 7.12 % Favored : 91.64 % 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: -1.32 (0.21), residues: 1428 helix: 0.15 (0.21), residues: 550 sheet: -2.37 (0.31), residues: 196 loop : -1.19 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 66 TYR 0.026 0.003 TYR B 238 PHE 0.028 0.003 PHE B 79 TRP 0.019 0.003 TRP D 125 HIS 0.006 0.002 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.34 (17406) covalent geometry : angle 0.77177 / 0.43 (24374) hydrogen bonds : bond 0.05680 / 3.76 ( 630) hydrogen bonds : angle 5.03439 / 3.52 ( 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 155 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.750 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: C 160 SER cc_start: 0.8360 (t) cc_final: 0.7980 (m) REVERT: C 291 LEU cc_start: 0.8540 (tt) cc_final: 0.8295 (tp) REVERT: D 127 GLU cc_start: 0.6321 (mm-30) cc_final: 0.6120 (mt-10) REVERT: D 160 SER cc_start: 0.8385 (t) cc_final: 0.7979 (m) REVERT: D 264 ASP cc_start: 0.8131 (t0) cc_final: 0.7914 (t0) REVERT: D 291 LEU cc_start: 0.8542 (tt) cc_final: 0.8298 (tp) outliers start: 16 outliers final: 12 residues processed: 149 average time/residue: 0.2505 time to fit residues: 55.9670 Evaluate side-chains 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 A residue 76 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 B residue 76 GLU Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 189 MET 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: 1.9990 chunk 44 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.211938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168886 restraints weight = 57408.883| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.44 r_work: 0.3745 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17406 Z= 0.133 Angle : 0.590 6.751 24374 Z= 0.339 Chirality : 0.041 0.187 2580 Planarity : 0.005 0.082 2308 Dihedral : 27.417 69.685 4094 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.24 % Allowed : 7.28 % Favored : 91.49 % 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: 0.64 (0.21), residues: 556 sheet: -2.23 (0.31), residues: 192 loop : -1.07 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.017 0.001 TYR C 87 PHE 0.013 0.001 PHE B 186 TRP 0.010 0.001 TRP D 308 HIS 0.003 0.001 HIS C 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (17406) covalent geometry : angle 0.59017 / 0.34 (24374) hydrogen bonds : bond 0.03843 / 2.52 ( 630) hydrogen bonds : angle 4.42387 / 3.10 ( 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 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: A 152 MET cc_start: 0.8193 (tpt) cc_final: 0.7379 (tpt) REVERT: B 69 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: B 152 MET cc_start: 0.8200 (tpt) cc_final: 0.7386 (tpt) REVERT: C 160 SER cc_start: 0.8326 (t) cc_final: 0.7930 (m) REVERT: C 264 ASP cc_start: 0.8048 (t0) cc_final: 0.7821 (t0) REVERT: C 291 LEU cc_start: 0.8564 (tt) cc_final: 0.8253 (tp) REVERT: D 160 SER cc_start: 0.8332 (t) cc_final: 0.7938 (m) REVERT: D 264 ASP cc_start: 0.8050 (t0) cc_final: 0.7813 (t0) REVERT: D 291 LEU cc_start: 0.8562 (tt) cc_final: 0.8251 (tp) outliers start: 16 outliers final: 8 residues processed: 140 average time/residue: 0.2363 time to fit residues: 51.0590 Evaluate side-chains 134 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 189 MET 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: 6.9990 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: 4.9990 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.205370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161436 restraints weight = 58063.518| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.53 r_work: 0.3680 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17406 Z= 0.230 Angle : 0.641 7.515 24374 Z= 0.361 Chirality : 0.043 0.232 2580 Planarity : 0.005 0.071 2308 Dihedral : 27.268 74.547 4094 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.39 % Allowed : 8.05 % 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: -1.01 (0.22), residues: 1428 helix: 0.51 (0.22), residues: 554 sheet: -2.27 (0.31), residues: 196 loop : -1.09 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.023 0.002 TYR C 87 PHE 0.022 0.002 PHE B 210 TRP 0.013 0.002 TRP C 125 HIS 0.005 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (17406) covalent geometry : angle 0.64094 / 0.36 (24374) hydrogen bonds : bond 0.04329 / 2.85 ( 630) hydrogen bonds : angle 4.59927 / 3.22 ( 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: 18 poor density : 121 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 133 average time/residue: 0.2416 time to fit residues: 49.0353 Evaluate side-chains 133 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 C residue 329 GLU Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 329 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.208135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164998 restraints weight = 58258.717| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.43 r_work: 0.3724 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17406 Z= 0.132 Angle : 0.568 6.232 24374 Z= 0.327 Chirality : 0.040 0.200 2580 Planarity : 0.005 0.068 2308 Dihedral : 27.171 72.056 4094 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.55 % Allowed : 7.82 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1428 helix: 0.84 (0.22), residues: 556 sheet: -2.33 (0.33), residues: 176 loop : -1.17 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.026 0.001 TYR D 87 PHE 0.014 0.001 PHE B 210 TRP 0.010 0.001 TRP C 308 HIS 0.003 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (17406) covalent geometry : angle 0.56760 / 0.33 (24374) hydrogen bonds : bond 0.03578 / 2.35 ( 630) hydrogen bonds : angle 4.32741 / 3.03 ( 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 143 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8063 (tpt) cc_final: 0.7234 (tpt) REVERT: B 9 MET cc_start: 0.7153 (mmm) cc_final: 0.6656 (mmm) REVERT: B 152 MET cc_start: 0.8063 (tpt) cc_final: 0.7233 (tpt) REVERT: C 291 LEU cc_start: 0.8547 (tt) cc_final: 0.8248 (tp) outliers start: 20 outliers final: 11 residues processed: 139 average time/residue: 0.2535 time to fit residues: 53.9542 Evaluate side-chains 137 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 147 optimal weight: 40.0000 chunk 70 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.205252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.161667 restraints weight = 58010.426| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.44 r_work: 0.3679 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17406 Z= 0.211 Angle : 0.620 7.622 24374 Z= 0.351 Chirality : 0.043 0.223 2580 Planarity : 0.005 0.064 2308 Dihedral : 27.112 76.795 4094 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.08 % Allowed : 8.28 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1428 helix: 0.58 (0.22), residues: 554 sheet: -2.41 (0.33), residues: 176 loop : -1.19 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.015 0.002 TYR A 238 PHE 0.019 0.002 PHE B 79 TRP 0.012 0.002 TRP C 125 HIS 0.003 0.001 HIS D 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (17406) covalent geometry : angle 0.62005 / 0.35 (24374) hydrogen bonds : bond 0.04174 / 2.76 ( 630) hydrogen bonds : angle 4.53992 / 3.18 ( 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 137 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8153 (tpt) cc_final: 0.7293 (tpt) REVERT: B 9 MET cc_start: 0.7229 (mmm) cc_final: 0.6665 (mmm) REVERT: B 152 MET cc_start: 0.8151 (tpt) cc_final: 0.7291 (tpt) outliers start: 14 outliers final: 13 residues processed: 133 average time/residue: 0.2376 time to fit residues: 48.3705 Evaluate side-chains 133 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain D residue 189 MET 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: 0.9980 chunk 155 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.205315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.162231 restraints weight = 58047.528| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.47 r_work: 0.3689 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17406 Z= 0.176 Angle : 0.588 7.187 24374 Z= 0.338 Chirality : 0.042 0.208 2580 Planarity : 0.005 0.062 2308 Dihedral : 27.019 76.847 4094 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.01 % Allowed : 8.44 % 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: -1.03 (0.22), residues: 1428 helix: 0.62 (0.22), residues: 554 sheet: -2.45 (0.33), residues: 176 loop : -1.24 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 16 TYR 0.025 0.001 TYR C 87 PHE 0.013 0.002 PHE B 210 TRP 0.011 0.001 TRP C 125 HIS 0.005 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (17406) covalent geometry : angle 0.58809 / 0.34 (24374) hydrogen bonds : bond 0.03787 / 2.50 ( 630) hydrogen bonds : angle 4.48386 / 3.14 ( 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 146 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8248 (tpt) cc_final: 0.7425 (tpt) REVERT: B 9 MET cc_start: 0.7404 (mmm) cc_final: 0.6892 (mmm) REVERT: B 152 MET cc_start: 0.8255 (tpt) cc_final: 0.7430 (tpt) REVERT: C 264 ASP cc_start: 0.8060 (t0) cc_final: 0.7799 (t0) REVERT: D 264 ASP cc_start: 0.8028 (t0) cc_final: 0.7789 (t0) outliers start: 13 outliers final: 12 residues processed: 143 average time/residue: 0.2521 time to fit residues: 54.3769 Evaluate side-chains 139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 265 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 189 MET 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: 0.7980 chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.208179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.165133 restraints weight = 58672.493| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.50 r_work: 0.3724 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17406 Z= 0.122 Angle : 0.555 6.384 24374 Z= 0.321 Chirality : 0.040 0.181 2580 Planarity : 0.004 0.058 2308 Dihedral : 26.885 77.425 4094 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.70 % Allowed : 8.82 % Favored : 90.48 % 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: -0.68 (0.22), residues: 1428 helix: 1.00 (0.22), residues: 556 sheet: -2.30 (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 0.013 0.001 TYR D 87 PHE 0.022 0.001 PHE D 157 TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (17406) covalent geometry : angle 0.55455 / 0.32 (24374) hydrogen bonds : bond 0.03317 / 2.19 ( 630) hydrogen bonds : angle 4.20994 / 2.95 ( 1676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6823.86 seconds wall clock time: 116 minutes 20.40 seconds (6980.40 seconds total)