Starting phenix.real_space_refine on Tue Mar 3 13:54:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6izv_9758/03_2026/6izv_9758.cif Found real_map, /net/cci-nas-00/data/ceres_data/6izv_9758/03_2026/6izv_9758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6izv_9758/03_2026/6izv_9758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6izv_9758/03_2026/6izv_9758.map" model { file = "/net/cci-nas-00/data/ceres_data/6izv_9758/03_2026/6izv_9758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6izv_9758/03_2026/6izv_9758.cif" } resolution = 4.2 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= 0.011 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 3578 2.51 5 N 940 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5624 Number of models: 1 Model: "" Number of chains: 4 Chain: "0" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "1" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.41, per 1000 atoms: 0.25 Number of scatterers: 5624 At special positions: 0 Unit cell: (73.205, 83.853, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 4 15.00 Mg 2 11.99 O 1080 8.00 N 940 7.00 C 3578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 296.5 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 40.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain '0' and resid 38 through 44 removed outlier: 3.703A pdb=" N PHE 0 42 " --> pdb=" O SER 0 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 0 43 " --> pdb=" O LEU 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 70 through 76 removed outlier: 3.525A pdb=" N ARG 0 75 " --> pdb=" O GLU 0 71 " (cutoff:3.500A) Processing helix chain '0' and resid 91 through 104 Processing helix chain '0' and resid 125 through 130 removed outlier: 4.437A pdb=" N LYS 0 129 " --> pdb=" O GLU 0 125 " (cutoff:3.500A) Processing helix chain '0' and resid 130 through 141 removed outlier: 4.271A pdb=" N LEU 0 134 " --> pdb=" O GLN 0 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS 0 139 " --> pdb=" O ASN 0 135 " (cutoff:3.500A) Processing helix chain '0' and resid 169 through 175 removed outlier: 4.352A pdb=" N ILE 0 173 " --> pdb=" O GLY 0 169 " (cutoff:3.500A) Processing helix chain '0' and resid 180 through 184 removed outlier: 3.970A pdb=" N SER 0 183 " --> pdb=" O ASP 0 180 " (cutoff:3.500A) Processing helix chain '0' and resid 229 through 245 removed outlier: 3.580A pdb=" N LYS 0 238 " --> pdb=" O ASN 0 234 " (cutoff:3.500A) Processing helix chain '0' and resid 251 through 262 removed outlier: 3.697A pdb=" N CYS 0 259 " --> pdb=" O LEU 0 255 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU 0 260 " --> pdb=" O MET 0 256 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 0 261 " --> pdb=" O LEU 0 257 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 296 removed outlier: 4.358A pdb=" N LYS 0 291 " --> pdb=" O ASN 0 287 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU 0 295 " --> pdb=" O LYS 0 291 " (cutoff:3.500A) Processing helix chain '0' and resid 297 through 301 removed outlier: 3.667A pdb=" N LYS 0 300 " --> pdb=" O GLY 0 297 " (cutoff:3.500A) Processing helix chain '0' and resid 310 through 317 removed outlier: 3.844A pdb=" N LYS 0 314 " --> pdb=" O GLY 0 310 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL 0 315 " --> pdb=" O GLY 0 311 " (cutoff:3.500A) Processing helix chain '0' and resid 319 through 324 removed outlier: 3.733A pdb=" N LEU 0 322 " --> pdb=" O HIS 0 319 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE 0 323 " --> pdb=" O LEU 0 320 " (cutoff:3.500A) Processing helix chain '0' and resid 336 through 345 Processing helix chain '1' and resid 38 through 44 removed outlier: 3.702A pdb=" N PHE 1 42 " --> pdb=" O SER 1 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE 1 43 " --> pdb=" O LEU 1 39 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 76 removed outlier: 3.524A pdb=" N ARG 1 75 " --> pdb=" O GLU 1 71 " (cutoff:3.500A) Processing helix chain '1' and resid 91 through 104 Processing helix chain '1' and resid 125 through 130 removed outlier: 4.437A pdb=" N LYS 1 129 " --> pdb=" O GLU 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 141 removed outlier: 4.271A pdb=" N LEU 1 134 " --> pdb=" O GLN 1 130 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS 1 139 " --> pdb=" O ASN 1 135 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 175 removed outlier: 4.352A pdb=" N ILE 1 173 " --> pdb=" O GLY 1 169 " (cutoff:3.500A) Processing helix chain '1' and resid 180 through 184 removed outlier: 3.969A pdb=" N SER 1 183 " --> pdb=" O ASP 1 180 " (cutoff:3.500A) Processing helix chain '1' and resid 229 through 245 removed outlier: 3.580A pdb=" N LYS 1 238 " --> pdb=" O ASN 1 234 " (cutoff:3.500A) Processing helix chain '1' and resid 251 through 262 removed outlier: 3.697A pdb=" N CYS 1 259 " --> pdb=" O LEU 1 255 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU 1 260 " --> pdb=" O MET 1 256 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 1 261 " --> pdb=" O LEU 1 257 " (cutoff:3.500A) Processing helix chain '1' and resid 273 through 296 removed outlier: 4.359A pdb=" N LYS 1 291 " --> pdb=" O ASN 1 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 1 295 " --> pdb=" O LYS 1 291 " (cutoff:3.500A) Processing helix chain '1' and resid 297 through 301 removed outlier: 3.667A pdb=" N LYS 1 300 " --> pdb=" O GLY 1 297 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 317 removed outlier: 3.844A pdb=" N LYS 1 314 " --> pdb=" O GLY 1 310 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL 1 315 " --> pdb=" O GLY 1 311 " (cutoff:3.500A) Processing helix chain '1' and resid 319 through 324 removed outlier: 3.733A pdb=" N LEU 1 322 " --> pdb=" O HIS 1 319 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE 1 323 " --> pdb=" O LEU 1 320 " (cutoff:3.500A) Processing helix chain '1' and resid 336 through 345 Processing sheet with id=AA1, first strand: chain '0' and resid 24 through 28 removed outlier: 6.182A pdb=" N TYR 0 4 " --> pdb=" O HIS 0 117 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL 0 119 " --> pdb=" O TYR 0 4 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE 0 6 " --> pdb=" O VAL 0 119 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY 0 121 " --> pdb=" O ILE 0 6 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ILE 0 8 " --> pdb=" O GLY 0 121 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE 0 166 " --> pdb=" O THR 0 120 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 0 122 " --> pdb=" O PHE 0 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain '0' and resid 214 through 216 Processing sheet with id=AA4, first strand: chain '0' and resid 214 through 216 removed outlier: 7.422A pdb=" N PHE 0 190 " --> pdb=" O SER 0 305 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N MET 0 307 " --> pdb=" O PHE 0 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY 0 192 " --> pdb=" O MET 0 307 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA 0 309 " --> pdb=" O GLY 0 192 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE 0 194 " --> pdb=" O ALA 0 309 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLN 0 329 " --> pdb=" O ASN 0 304 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE 0 306 " --> pdb=" O GLN 0 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '0' and resid 263 through 265 removed outlier: 3.784A pdb=" N ILE 0 264 " --> pdb=" O ILE 0 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 24 through 28 removed outlier: 6.184A pdb=" N TYR 1 4 " --> pdb=" O HIS 1 117 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL 1 119 " --> pdb=" O TYR 1 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE 1 6 " --> pdb=" O VAL 1 119 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY 1 121 " --> pdb=" O ILE 1 6 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ILE 1 8 " --> pdb=" O GLY 1 121 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE 1 166 " --> pdb=" O THR 1 120 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 1 122 " --> pdb=" O PHE 1 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 31 through 33 Processing sheet with id=AA8, first strand: chain '1' and resid 214 through 216 Processing sheet with id=AA9, first strand: chain '1' and resid 214 through 216 removed outlier: 7.422A pdb=" N PHE 1 190 " --> pdb=" O SER 1 305 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET 1 307 " --> pdb=" O PHE 1 190 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLY 1 192 " --> pdb=" O MET 1 307 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALA 1 309 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE 1 194 " --> pdb=" O ALA 1 309 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLN 1 329 " --> pdb=" O ASN 1 304 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE 1 306 " --> pdb=" O GLN 1 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 263 through 265 removed outlier: 3.784A pdb=" N ILE 1 264 " --> pdb=" O ILE 1 271 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1825 1.34 - 1.46: 1065 1.46 - 1.57: 2790 1.57 - 1.69: 6 1.69 - 1.80: 36 Bond restraints: 5722 Sorted by residual: bond pdb=" C ASN 0 162 " pdb=" N ILE 0 163 " ideal model delta sigma weight residual 1.334 1.316 0.018 1.29e-02 6.01e+03 1.92e+00 bond pdb=" C ASN 1 162 " pdb=" N ILE 1 163 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.81e+00 bond pdb=" C4 ADP 1 401 " pdb=" C5 ADP 1 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C4 ADP 0 401 " pdb=" C5 ADP 0 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CA VAL 1 196 " pdb=" CB VAL 1 196 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.36e+00 ... (remaining 5717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 7295 1.73 - 3.46: 357 3.46 - 5.19: 38 5.19 - 6.91: 12 6.91 - 8.64: 10 Bond angle restraints: 7712 Sorted by residual: angle pdb=" C SER 0 175 " pdb=" N LYS 0 176 " pdb=" CA LYS 0 176 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C SER 1 175 " pdb=" N LYS 1 176 " pdb=" CA LYS 1 176 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N ILE 0 83 " pdb=" CA ILE 0 83 " pdb=" C ILE 0 83 " ideal model delta sigma weight residual 113.42 109.34 4.08 1.17e+00 7.31e-01 1.22e+01 angle pdb=" N ILE 1 83 " pdb=" CA ILE 1 83 " pdb=" C ILE 1 83 " ideal model delta sigma weight residual 113.42 109.35 4.07 1.17e+00 7.31e-01 1.21e+01 angle pdb=" C PRO 0 325 " pdb=" N ASN 0 326 " pdb=" CA ASN 0 326 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 ... (remaining 7707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.87: 3412 29.87 - 59.74: 37 59.74 - 89.61: 8 89.61 - 119.48: 0 119.48 - 149.35: 1 Dihedral angle restraints: 3458 sinusoidal: 1446 harmonic: 2012 Sorted by residual: dihedral pdb=" O1B ADP 0 401 " pdb=" O3A ADP 0 401 " pdb=" PB ADP 0 401 " pdb=" PA ADP 0 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.64 149.35 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" CA CYS 0 259 " pdb=" C CYS 0 259 " pdb=" N GLU 0 260 " pdb=" CA GLU 0 260 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS 1 259 " pdb=" C CYS 1 259 " pdb=" N GLU 1 260 " pdb=" CA GLU 1 260 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 594 0.049 - 0.097: 205 0.097 - 0.146: 54 0.146 - 0.194: 3 0.194 - 0.242: 4 Chirality restraints: 860 Sorted by residual: chirality pdb=" CB VAL 0 55 " pdb=" CA VAL 0 55 " pdb=" CG1 VAL 0 55 " pdb=" CG2 VAL 0 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL 1 55 " pdb=" CA VAL 1 55 " pdb=" CG1 VAL 1 55 " pdb=" CG2 VAL 1 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE 0 26 " pdb=" CA ILE 0 26 " pdb=" CG1 ILE 0 26 " pdb=" CG2 ILE 0 26 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 857 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 0 345 " -0.016 2.00e-02 2.50e+03 1.85e-02 5.99e+00 pdb=" CG PHE 0 345 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 0 345 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE 0 345 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 0 345 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE 0 345 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE 0 345 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 345 " 0.016 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE 1 345 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 345 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 345 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 345 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 345 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE 1 345 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 1 148 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C VAL 1 148 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL 1 148 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP 1 149 " -0.011 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 214 2.72 - 3.26: 5427 3.26 - 3.81: 8816 3.81 - 4.35: 11096 4.35 - 4.90: 18565 Nonbonded interactions: 44118 Sorted by model distance: nonbonded pdb=" NE2 GLN 1 168 " pdb="MG MG 1 402 " model vdw 2.170 2.250 nonbonded pdb=" NE2 GLN 0 168 " pdb="MG MG 0 402 " model vdw 2.171 2.250 nonbonded pdb=" O1B ADP 1 401 " pdb="MG MG 1 402 " model vdw 2.265 2.170 nonbonded pdb=" O2B ADP 0 401 " pdb="MG MG 0 402 " model vdw 2.265 2.170 nonbonded pdb=" OH TYR 1 233 " pdb=" O2' ADP 1 401 " model vdw 2.281 3.040 ... (remaining 44113 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' } 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 group one per residue 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5722 Z= 0.237 Angle : 0.899 8.642 7712 Z= 0.495 Chirality : 0.052 0.242 860 Planarity : 0.005 0.038 992 Dihedral : 10.554 149.352 2158 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -3.60 (0.28), residues: 694 helix: -3.74 (0.19), residues: 218 sheet: -2.24 (0.39), residues: 176 loop : -1.09 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 0 37 TYR 0.010 0.002 TYR 1 270 PHE 0.038 0.003 PHE 0 345 TRP 0.015 0.004 TRP 0 296 HIS 0.007 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 5722) covalent geometry : angle 0.89948 ( 7712) hydrogen bonds : bond 0.27257 ( 202) hydrogen bonds : angle 9.75591 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 ILE cc_start: 0.9504 (mt) cc_final: 0.9271 (tp) REVERT: 0 71 GLU cc_start: 0.8288 (tp30) cc_final: 0.8014 (tp30) REVERT: 0 130 GLN cc_start: 0.8460 (mt0) cc_final: 0.8195 (mt0) REVERT: 0 135 ASN cc_start: 0.8874 (t0) cc_final: 0.8500 (m-40) REVERT: 0 193 LEU cc_start: 0.9151 (tp) cc_final: 0.8758 (tp) REVERT: 0 219 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7737 (tm-30) REVERT: 0 220 MET cc_start: 0.8694 (mtp) cc_final: 0.7974 (mtt) REVERT: 0 246 ASP cc_start: 0.8716 (t70) cc_final: 0.8161 (t70) REVERT: 0 256 MET cc_start: 0.8183 (mtp) cc_final: 0.7937 (tpt) REVERT: 0 261 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8635 (mm-30) REVERT: 1 130 GLN cc_start: 0.8053 (mt0) cc_final: 0.7834 (mt0) REVERT: 1 211 ASP cc_start: 0.8051 (m-30) cc_final: 0.7725 (t70) REVERT: 1 220 MET cc_start: 0.8062 (mtp) cc_final: 0.6376 (mtp) REVERT: 1 256 MET cc_start: 0.8304 (mtp) cc_final: 0.7905 (tpt) REVERT: 1 319 HIS cc_start: 0.8277 (m-70) cc_final: 0.8032 (m-70) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0980 time to fit residues: 25.6247 Evaluate side-chains 100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 overall best weight: 6.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN 0 52 ASN 0 150 HIS ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 14 GLN 1 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.061921 restraints weight = 17561.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064113 restraints weight = 10007.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.065675 restraints weight = 6754.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.066709 restraints weight = 5059.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067546 restraints weight = 4121.803| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5722 Z= 0.257 Angle : 0.778 7.305 7712 Z= 0.402 Chirality : 0.051 0.313 860 Planarity : 0.005 0.041 992 Dihedral : 9.061 102.486 754 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.98 % 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: -2.51 (0.31), residues: 694 helix: -1.75 (0.29), residues: 224 sheet: -2.12 (0.38), residues: 182 loop : -0.98 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 207 TYR 0.018 0.002 TYR 0 270 PHE 0.033 0.002 PHE 1 345 TRP 0.008 0.002 TRP 1 296 HIS 0.008 0.002 HIS 0 54 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 5722) covalent geometry : angle 0.77845 ( 7712) hydrogen bonds : bond 0.04430 ( 202) hydrogen bonds : angle 6.45041 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.228 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: 0 67 TYR cc_start: 0.8849 (m-80) cc_final: 0.8452 (m-80) REVERT: 0 71 GLU cc_start: 0.8588 (tp30) cc_final: 0.8383 (tp30) REVERT: 0 130 GLN cc_start: 0.8457 (mt0) cc_final: 0.8036 (mt0) REVERT: 0 135 ASN cc_start: 0.8628 (t0) cc_final: 0.7921 (m-40) REVERT: 0 137 MET cc_start: 0.8674 (tmm) cc_final: 0.8099 (tmm) REVERT: 0 139 LYS cc_start: 0.8483 (mtmt) cc_final: 0.7652 (ptpt) REVERT: 0 213 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8914 (mt-10) REVERT: 0 220 MET cc_start: 0.8282 (mtp) cc_final: 0.7945 (mtt) REVERT: 0 246 ASP cc_start: 0.8665 (t70) cc_final: 0.8096 (t0) REVERT: 0 327 MET cc_start: 0.8317 (ttp) cc_final: 0.8073 (ttp) REVERT: 1 67 TYR cc_start: 0.8942 (m-80) cc_final: 0.8569 (m-80) REVERT: 1 130 GLN cc_start: 0.8065 (mt0) cc_final: 0.7849 (mt0) REVERT: 1 136 ASP cc_start: 0.8646 (m-30) cc_final: 0.8197 (p0) REVERT: 1 137 MET cc_start: 0.7765 (ttm) cc_final: 0.7375 (ttm) REVERT: 1 211 ASP cc_start: 0.8172 (m-30) cc_final: 0.7815 (t70) REVERT: 1 220 MET cc_start: 0.7661 (mtp) cc_final: 0.7436 (mtp) REVERT: 1 256 MET cc_start: 0.8087 (mtp) cc_final: 0.7876 (tpt) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.0633 time to fit residues: 10.5655 Evaluate side-chains 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 43 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.075300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.062069 restraints weight = 17594.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.064269 restraints weight = 9993.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065847 restraints weight = 6701.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066944 restraints weight = 5002.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067735 restraints weight = 4044.447| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5722 Z= 0.214 Angle : 0.689 6.996 7712 Z= 0.353 Chirality : 0.047 0.187 860 Planarity : 0.004 0.037 992 Dihedral : 8.498 89.193 754 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.16 % Allowed : 2.89 % Favored : 96.95 % 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: -1.99 (0.32), residues: 694 helix: -0.99 (0.33), residues: 236 sheet: -2.01 (0.38), residues: 180 loop : -0.83 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 299 TYR 0.010 0.002 TYR 0 270 PHE 0.023 0.002 PHE 1 345 TRP 0.005 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5722) covalent geometry : angle 0.68913 ( 7712) hydrogen bonds : bond 0.03873 ( 202) hydrogen bonds : angle 5.97209 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8533 (mt0) cc_final: 0.8322 (mt0) REVERT: 0 137 MET cc_start: 0.8783 (tmm) cc_final: 0.8221 (tmm) REVERT: 0 139 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8211 (mtpt) REVERT: 0 213 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8958 (mt-10) REVERT: 0 218 GLN cc_start: 0.8384 (tt0) cc_final: 0.8178 (mt0) REVERT: 0 220 MET cc_start: 0.7877 (mtp) cc_final: 0.7648 (mtt) REVERT: 0 246 ASP cc_start: 0.8590 (t70) cc_final: 0.8164 (t70) REVERT: 0 317 TYR cc_start: 0.9135 (t80) cc_final: 0.8788 (t80) REVERT: 0 327 MET cc_start: 0.8328 (ttp) cc_final: 0.8073 (ttp) REVERT: 1 67 TYR cc_start: 0.8894 (m-80) cc_final: 0.8440 (m-80) REVERT: 1 130 GLN cc_start: 0.8102 (mt0) cc_final: 0.7876 (mt0) REVERT: 1 136 ASP cc_start: 0.8681 (m-30) cc_final: 0.7999 (p0) REVERT: 1 137 MET cc_start: 0.7879 (ttm) cc_final: 0.7507 (ttm) REVERT: 1 211 ASP cc_start: 0.7959 (m-30) cc_final: 0.7653 (t70) REVERT: 1 218 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8108 (tm-30) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.0647 time to fit residues: 9.4433 Evaluate side-chains 81 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN 0 52 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.061033 restraints weight = 17850.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063055 restraints weight = 10080.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064511 restraints weight = 6766.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065484 restraints weight = 5055.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066203 restraints weight = 4103.779| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5722 Z= 0.189 Angle : 0.672 8.345 7712 Z= 0.339 Chirality : 0.046 0.146 860 Planarity : 0.004 0.055 992 Dihedral : 7.964 81.146 754 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.68 (0.32), residues: 694 helix: -0.62 (0.35), residues: 234 sheet: -1.89 (0.39), residues: 170 loop : -0.79 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 85 TYR 0.020 0.002 TYR 1 317 PHE 0.025 0.002 PHE 1 345 TRP 0.003 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 5722) covalent geometry : angle 0.67172 ( 7712) hydrogen bonds : bond 0.03422 ( 202) hydrogen bonds : angle 5.59199 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8572 (mt0) cc_final: 0.8069 (mt0) REVERT: 0 137 MET cc_start: 0.8760 (tmm) cc_final: 0.8113 (tmm) REVERT: 0 246 ASP cc_start: 0.8436 (t70) cc_final: 0.7996 (t70) REVERT: 0 317 TYR cc_start: 0.9150 (t80) cc_final: 0.8775 (t80) REVERT: 1 49 ILE cc_start: 0.8998 (tt) cc_final: 0.8798 (tt) REVERT: 1 67 TYR cc_start: 0.8740 (m-80) cc_final: 0.8327 (m-80) REVERT: 1 130 GLN cc_start: 0.8188 (mt0) cc_final: 0.7919 (mt0) REVERT: 1 136 ASP cc_start: 0.8652 (m-30) cc_final: 0.7856 (p0) REVERT: 1 137 MET cc_start: 0.8059 (ttm) cc_final: 0.7392 (ttm) REVERT: 1 211 ASP cc_start: 0.7960 (m-30) cc_final: 0.7749 (t70) REVERT: 1 218 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8107 (tm-30) REVERT: 1 256 MET cc_start: 0.8091 (tmm) cc_final: 0.7786 (tpt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0610 time to fit residues: 8.2857 Evaluate side-chains 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 overall best weight: 3.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 218 GLN 1 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063984 restraints weight = 17818.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066299 restraints weight = 9889.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067906 restraints weight = 6535.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069041 restraints weight = 4826.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069805 restraints weight = 3868.618| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5722 Z= 0.152 Angle : 0.643 8.038 7712 Z= 0.326 Chirality : 0.045 0.149 860 Planarity : 0.003 0.032 992 Dihedral : 7.544 77.537 754 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.26 (0.33), residues: 694 helix: -0.15 (0.37), residues: 216 sheet: -1.77 (0.41), residues: 160 loop : -0.63 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 85 TYR 0.019 0.002 TYR 1 317 PHE 0.022 0.002 PHE 1 345 TRP 0.001 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5722) covalent geometry : angle 0.64340 ( 7712) hydrogen bonds : bond 0.03182 ( 202) hydrogen bonds : angle 5.54053 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8656 (mt0) cc_final: 0.8138 (mt0) REVERT: 0 137 MET cc_start: 0.8707 (tmm) cc_final: 0.8107 (tmm) REVERT: 0 246 ASP cc_start: 0.8541 (t70) cc_final: 0.8082 (t70) REVERT: 0 317 TYR cc_start: 0.9177 (t80) cc_final: 0.8807 (t80) REVERT: 1 67 TYR cc_start: 0.8808 (m-80) cc_final: 0.8535 (m-80) REVERT: 1 136 ASP cc_start: 0.8598 (m-30) cc_final: 0.7834 (p0) REVERT: 1 137 MET cc_start: 0.6954 (ttm) cc_final: 0.6409 (ttm) REVERT: 1 211 ASP cc_start: 0.8027 (m-30) cc_final: 0.7727 (t70) REVERT: 1 218 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8111 (tm-30) REVERT: 1 256 MET cc_start: 0.8078 (tmm) cc_final: 0.7653 (tpt) REVERT: 1 261 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8208 (mm-30) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0571 time to fit residues: 8.2760 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 62 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.075675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.062807 restraints weight = 17722.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065025 restraints weight = 9926.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066612 restraints weight = 6574.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067736 restraints weight = 4853.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068485 restraints weight = 3871.100| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5722 Z= 0.192 Angle : 0.657 7.382 7712 Z= 0.332 Chirality : 0.045 0.146 860 Planarity : 0.003 0.029 992 Dihedral : 7.454 75.927 754 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -1.36 (0.33), residues: 694 helix: -0.27 (0.35), residues: 228 sheet: -1.77 (0.42), residues: 160 loop : -0.69 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 1 299 TYR 0.022 0.002 TYR 1 317 PHE 0.031 0.002 PHE 1 345 TRP 0.002 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5722) covalent geometry : angle 0.65675 ( 7712) hydrogen bonds : bond 0.03377 ( 202) hydrogen bonds : angle 5.55824 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8624 (mt0) cc_final: 0.8293 (mt0) REVERT: 0 137 MET cc_start: 0.8667 (tmm) cc_final: 0.8083 (tmm) REVERT: 0 246 ASP cc_start: 0.8615 (t70) cc_final: 0.8251 (t70) REVERT: 0 317 TYR cc_start: 0.9208 (t80) cc_final: 0.8783 (t80) REVERT: 1 168 GLN cc_start: 0.9122 (mt0) cc_final: 0.8830 (mt0) REVERT: 1 211 ASP cc_start: 0.8108 (m-30) cc_final: 0.7835 (t70) REVERT: 1 218 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8255 (tm-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0593 time to fit residues: 7.9217 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN 0 52 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063154 restraints weight = 17832.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.065454 restraints weight = 9937.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067063 restraints weight = 6568.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068224 restraints weight = 4835.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069050 restraints weight = 3842.996| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5722 Z= 0.175 Angle : 0.641 6.842 7712 Z= 0.324 Chirality : 0.045 0.147 860 Planarity : 0.003 0.029 992 Dihedral : 7.324 73.379 754 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -1.14 (0.33), residues: 694 helix: -0.05 (0.37), residues: 216 sheet: -1.68 (0.43), residues: 160 loop : -0.57 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 85 TYR 0.024 0.002 TYR 0 61 PHE 0.023 0.002 PHE 1 345 TRP 0.002 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5722) covalent geometry : angle 0.64135 ( 7712) hydrogen bonds : bond 0.03231 ( 202) hydrogen bonds : angle 5.56993 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 60 GLU cc_start: 0.8003 (pp20) cc_final: 0.7100 (pm20) REVERT: 0 130 GLN cc_start: 0.8690 (mt0) cc_final: 0.8357 (mt0) REVERT: 0 137 MET cc_start: 0.8644 (tmm) cc_final: 0.8090 (tmm) REVERT: 0 246 ASP cc_start: 0.8506 (t70) cc_final: 0.8230 (t70) REVERT: 0 317 TYR cc_start: 0.9305 (t80) cc_final: 0.8994 (t80) REVERT: 1 168 GLN cc_start: 0.9133 (mt0) cc_final: 0.8891 (mt0) REVERT: 1 211 ASP cc_start: 0.8117 (m-30) cc_final: 0.7793 (t70) REVERT: 1 218 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8090 (tm-30) REVERT: 1 256 MET cc_start: 0.7908 (tmm) cc_final: 0.7521 (tmm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0583 time to fit residues: 7.4025 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 52 ASN ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.064513 restraints weight = 17499.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066834 restraints weight = 9831.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068468 restraints weight = 6521.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069611 restraints weight = 4823.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.070431 restraints weight = 3857.131| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5722 Z= 0.143 Angle : 0.623 9.046 7712 Z= 0.314 Chirality : 0.045 0.148 860 Planarity : 0.003 0.028 992 Dihedral : 7.079 69.916 754 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -1.03 (0.33), residues: 694 helix: 0.09 (0.37), residues: 216 sheet: -1.34 (0.46), residues: 142 loop : -0.78 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 85 TYR 0.017 0.001 TYR 1 317 PHE 0.018 0.002 PHE 1 345 TRP 0.002 0.001 TRP 1 296 HIS 0.005 0.001 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5722) covalent geometry : angle 0.62310 ( 7712) hydrogen bonds : bond 0.03096 ( 202) hydrogen bonds : angle 5.53462 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 60 GLU cc_start: 0.8267 (pp20) cc_final: 0.6930 (pm20) REVERT: 0 130 GLN cc_start: 0.8692 (mt0) cc_final: 0.8155 (mt0) REVERT: 0 137 MET cc_start: 0.8631 (tmm) cc_final: 0.8088 (tmm) REVERT: 0 246 ASP cc_start: 0.8546 (t70) cc_final: 0.8280 (t70) REVERT: 0 317 TYR cc_start: 0.9223 (t80) cc_final: 0.8800 (t80) REVERT: 1 168 GLN cc_start: 0.9174 (mt0) cc_final: 0.8911 (mt0) REVERT: 1 211 ASP cc_start: 0.8105 (m-30) cc_final: 0.7819 (t70) REVERT: 1 218 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7918 (tm-30) REVERT: 1 225 ASP cc_start: 0.8358 (t70) cc_final: 0.8146 (t0) REVERT: 1 256 MET cc_start: 0.7963 (tmm) cc_final: 0.7588 (tmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0666 time to fit residues: 8.2819 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 0.0370 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 16 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064400 restraints weight = 17570.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066722 restraints weight = 9815.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068338 restraints weight = 6500.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069502 restraints weight = 4788.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.070337 restraints weight = 3806.279| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5722 Z= 0.144 Angle : 0.640 7.636 7712 Z= 0.320 Chirality : 0.045 0.148 860 Planarity : 0.003 0.027 992 Dihedral : 6.923 66.649 754 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.95 (0.33), residues: 694 helix: 0.16 (0.37), residues: 214 sheet: -1.29 (0.41), residues: 166 loop : -0.66 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 85 TYR 0.021 0.002 TYR 0 61 PHE 0.019 0.002 PHE 1 345 TRP 0.001 0.001 TRP 0 296 HIS 0.005 0.001 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5722) covalent geometry : angle 0.64036 ( 7712) hydrogen bonds : bond 0.03092 ( 202) hydrogen bonds : angle 5.57718 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8674 (mt0) cc_final: 0.8169 (mt0) REVERT: 0 137 MET cc_start: 0.8638 (tmm) cc_final: 0.8100 (tmm) REVERT: 0 242 ASP cc_start: 0.8934 (m-30) cc_final: 0.8707 (m-30) REVERT: 0 246 ASP cc_start: 0.8568 (t70) cc_final: 0.8278 (t70) REVERT: 0 317 TYR cc_start: 0.9200 (t80) cc_final: 0.8815 (t80) REVERT: 1 168 GLN cc_start: 0.9178 (mt0) cc_final: 0.8934 (mt0) REVERT: 1 211 ASP cc_start: 0.8126 (m-30) cc_final: 0.7811 (t0) REVERT: 1 218 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7818 (tm-30) REVERT: 1 225 ASP cc_start: 0.8304 (t70) cc_final: 0.8103 (t0) REVERT: 1 256 MET cc_start: 0.7984 (tmm) cc_final: 0.7576 (tmm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0639 time to fit residues: 8.2693 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063279 restraints weight = 18083.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065557 restraints weight = 10032.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067154 restraints weight = 6623.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068326 restraints weight = 4871.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069067 restraints weight = 3862.118| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5722 Z= 0.196 Angle : 0.669 7.173 7712 Z= 0.337 Chirality : 0.045 0.143 860 Planarity : 0.003 0.028 992 Dihedral : 6.992 64.964 754 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.33), residues: 694 helix: 0.15 (0.37), residues: 212 sheet: -1.35 (0.41), residues: 166 loop : -0.75 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 37 TYR 0.024 0.002 TYR 1 4 PHE 0.025 0.002 PHE 1 345 TRP 0.002 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5722) covalent geometry : angle 0.66889 ( 7712) hydrogen bonds : bond 0.03437 ( 202) hydrogen bonds : angle 5.64787 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8608 (mt0) cc_final: 0.8245 (mt0) REVERT: 0 137 MET cc_start: 0.8653 (tmm) cc_final: 0.8104 (tmm) REVERT: 0 242 ASP cc_start: 0.8961 (m-30) cc_final: 0.8731 (m-30) REVERT: 0 261 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8269 (mm-30) REVERT: 0 317 TYR cc_start: 0.9247 (t80) cc_final: 0.8878 (t80) REVERT: 1 168 GLN cc_start: 0.9189 (mt0) cc_final: 0.8949 (mt0) REVERT: 1 211 ASP cc_start: 0.8178 (m-30) cc_final: 0.7916 (t70) REVERT: 1 218 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8114 (tm-30) REVERT: 1 225 ASP cc_start: 0.8345 (t70) cc_final: 0.8145 (t0) REVERT: 1 256 MET cc_start: 0.7931 (tmm) cc_final: 0.7535 (tmm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0771 time to fit residues: 9.4501 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 39 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 14 GLN ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062652 restraints weight = 17618.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064860 restraints weight = 9892.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066496 restraints weight = 6535.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067627 restraints weight = 4789.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.068431 restraints weight = 3789.881| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5722 Z= 0.205 Angle : 0.693 7.331 7712 Z= 0.348 Chirality : 0.046 0.146 860 Planarity : 0.003 0.026 992 Dihedral : 7.048 63.954 754 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.07 (0.33), residues: 694 helix: 0.24 (0.38), residues: 210 sheet: -1.23 (0.42), residues: 156 loop : -0.97 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 0 299 TYR 0.022 0.002 TYR 1 4 PHE 0.025 0.002 PHE 1 345 TRP 0.002 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 5722) covalent geometry : angle 0.69286 ( 7712) hydrogen bonds : bond 0.03398 ( 202) hydrogen bonds : angle 5.67082 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 859.92 seconds wall clock time: 15 minutes 36.14 seconds (936.14 seconds total)