Starting phenix.real_space_refine on Sun Apr 27 12:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6izv_9758/04_2025/6izv_9758.cif Found real_map, /net/cci-nas-00/data/ceres_data/6izv_9758/04_2025/6izv_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_9758/04_2025/6izv_9758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6izv_9758/04_2025/6izv_9758.map" model { file = "/net/cci-nas-00/data/ceres_data/6izv_9758/04_2025/6izv_9758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6izv_9758/04_2025/6izv_9758.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 3.57, per 1000 atoms: 0.63 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: 1.38 Conformation dependent library (CDL) restraints added in 653.5 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: 0.68 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: 1.64 Time building geometry restraints manager: 1.51 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: 0.03 Found NCS groups: ncs_group { reference = chain '1' selection = chain '0' } 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: 0.050 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.004 TRP 0 296 HIS 0.007 0.002 HIS 1 54 PHE 0.038 0.003 PHE 0 345 TYR 0.010 0.002 TYR 1 270 ARG 0.003 0.001 ARG 0 37 Details of bonding type rmsd hydrogen bonds : bond 0.27257 ( 202) hydrogen bonds : angle 9.75591 ( 576) covalent geometry : bond 0.00474 ( 5722) covalent geometry : angle 0.89948 ( 7712) *********************** 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 : 0.594 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: 0.9270 (tp) REVERT: 0 71 GLU cc_start: 0.8287 (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: 0.8693 (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: 0.7938 (tpt) REVERT: 0 261 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8634 (mm-30) REVERT: 1 130 GLN cc_start: 0.8053 (mt0) cc_final: 0.7834 (mt0) REVERT: 1 211 ASP cc_start: 0.8052 (m-30) cc_final: 0.7725 (t70) REVERT: 1 220 MET cc_start: 0.8062 (mtp) cc_final: 0.6374 (mtp) REVERT: 1 256 MET cc_start: 0.8304 (mtp) cc_final: 0.7920 (tpt) REVERT: 1 319 HIS cc_start: 0.8278 (m-70) cc_final: 0.8036 (m-70) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2233 time to fit residues: 57.9068 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 : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.062650 restraints weight = 17323.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.064857 restraints weight = 9896.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066443 restraints weight = 6687.145| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5722 Z= 0.235 Angle : 0.760 6.777 7712 Z= 0.393 Chirality : 0.050 0.305 860 Planarity : 0.005 0.038 992 Dihedral : 9.004 101.451 754 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.31), residues: 694 helix: -1.65 (0.30), residues: 212 sheet: -2.09 (0.38), residues: 182 loop : -0.88 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP 1 296 HIS 0.009 0.002 HIS 0 54 PHE 0.032 0.002 PHE 1 345 TYR 0.017 0.002 TYR 0 270 ARG 0.005 0.001 ARG 1 207 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 202) hydrogen bonds : angle 6.39078 ( 576) covalent geometry : bond 0.00507 ( 5722) covalent geometry : angle 0.76041 ( 7712) *********************** 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 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 TYR cc_start: 0.7716 (t80) cc_final: 0.7187 (t80) REVERT: 0 60 GLU cc_start: 0.8561 (pt0) cc_final: 0.8319 (pm20) REVERT: 0 67 TYR cc_start: 0.8887 (m-80) cc_final: 0.8436 (m-80) REVERT: 0 71 GLU cc_start: 0.8529 (tp30) cc_final: 0.8313 (tp30) REVERT: 0 130 GLN cc_start: 0.8526 (mt0) cc_final: 0.8134 (mt0) REVERT: 0 135 ASN cc_start: 0.8603 (t0) cc_final: 0.7926 (m-40) REVERT: 0 137 MET cc_start: 0.8666 (tmm) cc_final: 0.8100 (tmm) REVERT: 0 139 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7580 (ptpt) REVERT: 0 213 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8920 (mt-10) REVERT: 0 220 MET cc_start: 0.8366 (mtp) cc_final: 0.8034 (mtt) REVERT: 0 246 ASP cc_start: 0.8715 (t70) cc_final: 0.8131 (t0) REVERT: 0 327 MET cc_start: 0.8331 (ttp) cc_final: 0.8093 (ttp) REVERT: 1 67 TYR cc_start: 0.8947 (m-80) cc_final: 0.8589 (m-80) REVERT: 1 130 GLN cc_start: 0.8064 (mt0) cc_final: 0.7846 (mt0) REVERT: 1 136 ASP cc_start: 0.8724 (m-30) cc_final: 0.8210 (p0) REVERT: 1 137 MET cc_start: 0.7744 (ttm) cc_final: 0.7454 (ttm) REVERT: 1 145 ILE cc_start: 0.8730 (tt) cc_final: 0.8528 (tt) REVERT: 1 211 ASP cc_start: 0.8218 (m-30) cc_final: 0.7852 (t70) REVERT: 1 220 MET cc_start: 0.7635 (mtp) cc_final: 0.7408 (mtp) REVERT: 1 256 MET cc_start: 0.8080 (mtp) cc_final: 0.7868 (tpt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1630 time to fit residues: 26.6814 Evaluate side-chains 78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 0.1980 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.2564 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063454 restraints weight = 17117.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.065690 restraints weight = 9653.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067268 restraints weight = 6428.928| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5722 Z= 0.178 Angle : 0.653 6.336 7712 Z= 0.336 Chirality : 0.046 0.149 860 Planarity : 0.004 0.035 992 Dihedral : 8.388 90.215 754 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.16 % Allowed : 2.09 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.32), residues: 694 helix: -0.98 (0.33), residues: 236 sheet: -1.96 (0.38), residues: 180 loop : -0.83 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 PHE 0.019 0.002 PHE 1 174 TYR 0.009 0.001 TYR 0 270 ARG 0.004 0.001 ARG 0 37 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 202) hydrogen bonds : angle 5.89809 ( 576) covalent geometry : bond 0.00393 ( 5722) covalent geometry : angle 0.65304 ( 7712) *********************** 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 109 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 104 LEU cc_start: 0.9541 (mp) cc_final: 0.9340 (mp) REVERT: 0 130 GLN cc_start: 0.8546 (mt0) cc_final: 0.8329 (mt0) REVERT: 0 135 ASN cc_start: 0.8678 (t0) cc_final: 0.7979 (m-40) REVERT: 0 137 MET cc_start: 0.8775 (tmm) cc_final: 0.8080 (tmm) REVERT: 0 139 LYS cc_start: 0.8421 (mtmt) cc_final: 0.7529 (ptpt) REVERT: 0 213 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8971 (mt-10) REVERT: 0 218 GLN cc_start: 0.8235 (tt0) cc_final: 0.8000 (mt0) REVERT: 0 220 MET cc_start: 0.7864 (mtp) cc_final: 0.7582 (mtt) REVERT: 0 246 ASP cc_start: 0.8686 (t70) cc_final: 0.8269 (t70) REVERT: 0 317 TYR cc_start: 0.9121 (t80) cc_final: 0.8792 (t80) REVERT: 0 327 MET cc_start: 0.8321 (ttp) cc_final: 0.8077 (ttp) REVERT: 1 67 TYR cc_start: 0.8874 (m-80) cc_final: 0.8470 (m-80) REVERT: 1 130 GLN cc_start: 0.8094 (mt0) cc_final: 0.7876 (mt0) REVERT: 1 136 ASP cc_start: 0.8706 (m-30) cc_final: 0.8095 (p0) REVERT: 1 137 MET cc_start: 0.7864 (ttm) cc_final: 0.7380 (ttm) REVERT: 1 211 ASP cc_start: 0.7974 (m-30) cc_final: 0.7667 (t70) REVERT: 1 218 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8266 (tm-30) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1456 time to fit residues: 21.7037 Evaluate side-chains 79 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** 1 162 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 = 0.3200 r_free = 0.3200 target = 0.073947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060830 restraints weight = 18170.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063062 restraints weight = 10205.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064600 restraints weight = 6793.132| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5722 Z= 0.244 Angle : 0.720 8.051 7712 Z= 0.366 Chirality : 0.047 0.144 860 Planarity : 0.004 0.051 992 Dihedral : 8.084 82.074 754 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.32), residues: 694 helix: -0.93 (0.34), residues: 240 sheet: -1.99 (0.38), residues: 180 loop : -0.69 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 1 296 HIS 0.006 0.002 HIS 1 54 PHE 0.034 0.002 PHE 1 345 TYR 0.021 0.002 TYR 1 317 ARG 0.003 0.000 ARG 1 207 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 202) hydrogen bonds : angle 5.73144 ( 576) covalent geometry : bond 0.00532 ( 5722) covalent geometry : angle 0.72034 ( 7712) *********************** 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 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 56 LYS cc_start: 0.7827 (mttm) cc_final: 0.7595 (mttm) REVERT: 0 60 GLU cc_start: 0.8463 (pp20) cc_final: 0.7349 (pm20) REVERT: 0 130 GLN cc_start: 0.8522 (mt0) cc_final: 0.8146 (mt0) REVERT: 0 137 MET cc_start: 0.8743 (tmm) cc_final: 0.8084 (tmm) REVERT: 0 220 MET cc_start: 0.7898 (mtp) cc_final: 0.7696 (mtt) REVERT: 0 246 ASP cc_start: 0.8634 (t70) cc_final: 0.8157 (t70) REVERT: 0 261 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8478 (mm-30) REVERT: 0 317 TYR cc_start: 0.9148 (t80) cc_final: 0.8765 (t80) REVERT: 1 49 ILE cc_start: 0.9004 (tt) cc_final: 0.8775 (tt) REVERT: 1 67 TYR cc_start: 0.8834 (m-80) cc_final: 0.8419 (m-80) REVERT: 1 130 GLN cc_start: 0.8130 (mt0) cc_final: 0.7831 (mt0) REVERT: 1 136 ASP cc_start: 0.8809 (m-30) cc_final: 0.7977 (p0) REVERT: 1 137 MET cc_start: 0.8055 (ttm) cc_final: 0.7450 (ttm) REVERT: 1 211 ASP cc_start: 0.8019 (m-30) cc_final: 0.7767 (t70) REVERT: 1 218 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8304 (tm-30) REVERT: 1 256 MET cc_start: 0.8076 (tmm) cc_final: 0.7761 (tpt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1513 time to fit residues: 20.5856 Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3261 r_free = 0.3261 target = 0.076937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063863 restraints weight = 17461.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066144 restraints weight = 9808.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067767 restraints weight = 6500.703| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5722 Z= 0.158 Angle : 0.652 7.791 7712 Z= 0.332 Chirality : 0.045 0.148 860 Planarity : 0.003 0.026 992 Dihedral : 7.673 78.564 754 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.33), residues: 694 helix: -0.46 (0.36), residues: 224 sheet: -1.65 (0.42), residues: 150 loop : -0.64 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 PHE 0.025 0.002 PHE 1 345 TYR 0.016 0.002 TYR 1 317 ARG 0.004 0.001 ARG 1 85 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 202) hydrogen bonds : angle 5.57749 ( 576) covalent geometry : bond 0.00352 ( 5722) covalent geometry : angle 0.65174 ( 7712) *********************** 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 102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 130 GLN cc_start: 0.8701 (mt0) cc_final: 0.8337 (mt0) REVERT: 0 135 ASN cc_start: 0.8662 (t0) cc_final: 0.7651 (m110) REVERT: 0 137 MET cc_start: 0.8744 (tmm) cc_final: 0.8164 (tmm) REVERT: 0 139 LYS cc_start: 0.8464 (mtmt) cc_final: 0.7829 (ptpt) REVERT: 0 220 MET cc_start: 0.7616 (mtp) cc_final: 0.7361 (mtt) REVERT: 0 246 ASP cc_start: 0.8599 (t70) cc_final: 0.8207 (t70) REVERT: 0 317 TYR cc_start: 0.9147 (t80) cc_final: 0.8773 (t80) REVERT: 1 67 TYR cc_start: 0.8762 (m-80) cc_final: 0.8461 (m-80) REVERT: 1 130 GLN cc_start: 0.8176 (mt0) cc_final: 0.7954 (mt0) REVERT: 1 136 ASP cc_start: 0.8703 (m-30) cc_final: 0.7844 (p0) REVERT: 1 142 GLU cc_start: 0.8305 (tp30) cc_final: 0.7606 (pm20) REVERT: 1 211 ASP cc_start: 0.8091 (m-30) cc_final: 0.7800 (t70) REVERT: 1 218 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8144 (tm-30) REVERT: 1 236 MET cc_start: 0.9044 (mmm) cc_final: 0.8839 (mmm) REVERT: 1 256 MET cc_start: 0.8016 (tmm) cc_final: 0.7603 (tpt) REVERT: 1 261 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8148 (mm-30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1642 time to fit residues: 22.8173 Evaluate side-chains 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 6 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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** 0 319 HIS 1 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.073056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060109 restraints weight = 18004.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062278 restraints weight = 10284.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063816 restraints weight = 6918.782| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5722 Z= 0.291 Angle : 0.758 9.128 7712 Z= 0.384 Chirality : 0.048 0.143 860 Planarity : 0.004 0.037 992 Dihedral : 7.841 77.156 754 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.32), residues: 694 helix: -1.01 (0.32), residues: 254 sheet: -1.87 (0.38), residues: 180 loop : -0.64 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 1 296 HIS 0.007 0.002 HIS 0 143 PHE 0.035 0.002 PHE 1 345 TYR 0.016 0.002 TYR 1 317 ARG 0.007 0.001 ARG 1 85 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 202) hydrogen bonds : angle 5.92006 ( 576) covalent geometry : bond 0.00640 ( 5722) covalent geometry : angle 0.75767 ( 7712) *********************** 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 92 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 56 LYS cc_start: 0.7879 (mttm) cc_final: 0.7561 (mttm) REVERT: 0 135 ASN cc_start: 0.8670 (t0) cc_final: 0.8261 (m110) REVERT: 0 137 MET cc_start: 0.8776 (tmm) cc_final: 0.8292 (tmm) REVERT: 0 213 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8917 (mt-10) REVERT: 0 220 MET cc_start: 0.7637 (mtp) cc_final: 0.7413 (mtt) REVERT: 0 317 TYR cc_start: 0.9263 (t80) cc_final: 0.8939 (t80) REVERT: 1 4 TYR cc_start: 0.8214 (t80) cc_final: 0.7991 (t80) REVERT: 1 130 GLN cc_start: 0.8100 (mt0) cc_final: 0.7798 (mt0) REVERT: 1 211 ASP cc_start: 0.8281 (m-30) cc_final: 0.7965 (t70) REVERT: 1 218 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8329 (tm-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1849 time to fit residues: 23.2093 Evaluate side-chains 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.075475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062251 restraints weight = 17701.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.064444 restraints weight = 10101.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066051 restraints weight = 6785.928| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5722 Z= 0.174 Angle : 0.665 7.044 7712 Z= 0.335 Chirality : 0.046 0.147 860 Planarity : 0.003 0.030 992 Dihedral : 7.514 74.670 754 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.33), residues: 694 helix: -0.50 (0.35), residues: 236 sheet: -1.72 (0.42), residues: 160 loop : -0.67 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 0 296 HIS 0.006 0.002 HIS 1 54 PHE 0.021 0.002 PHE 1 345 TYR 0.014 0.002 TYR 1 317 ARG 0.006 0.001 ARG 1 85 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 202) hydrogen bonds : angle 5.95985 ( 576) covalent geometry : bond 0.00384 ( 5722) covalent geometry : angle 0.66462 ( 7712) *********************** 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 94 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 135 ASN cc_start: 0.8624 (t0) cc_final: 0.7805 (m110) REVERT: 0 137 MET cc_start: 0.8770 (tmm) cc_final: 0.8099 (tmm) REVERT: 0 139 LYS cc_start: 0.8518 (mtmt) cc_final: 0.7927 (ptpt) REVERT: 0 220 MET cc_start: 0.7497 (mtp) cc_final: 0.7226 (mtt) REVERT: 0 317 TYR cc_start: 0.9272 (t80) cc_final: 0.8948 (t80) REVERT: 1 211 ASP cc_start: 0.8176 (m-30) cc_final: 0.7880 (t70) REVERT: 1 218 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8226 (tm-30) REVERT: 1 236 MET cc_start: 0.9020 (mmm) cc_final: 0.8807 (mmm) REVERT: 1 256 MET cc_start: 0.8025 (tmm) cc_final: 0.7686 (tmm) REVERT: 1 261 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8110 (mm-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1525 time to fit residues: 19.6091 Evaluate side-chains 61 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 0.0020 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 20 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.061524 restraints weight = 17755.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063689 restraints weight = 10211.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065217 restraints weight = 6902.233| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5572 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= 0.187 Angle : 0.671 9.290 7712 Z= 0.341 Chirality : 0.046 0.145 860 Planarity : 0.003 0.030 992 Dihedral : 7.423 72.363 754 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.33), residues: 694 helix: -0.43 (0.35), residues: 236 sheet: -1.54 (0.44), residues: 150 loop : -0.86 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 1 296 HIS 0.006 0.002 HIS 1 54 PHE 0.021 0.002 PHE 1 345 TYR 0.013 0.002 TYR 1 317 ARG 0.006 0.001 ARG 1 299 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 202) hydrogen bonds : angle 5.79675 ( 576) covalent geometry : bond 0.00411 ( 5722) covalent geometry : angle 0.67087 ( 7712) *********************** 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 86 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 135 ASN cc_start: 0.8625 (t0) cc_final: 0.8407 (m110) REVERT: 0 137 MET cc_start: 0.8775 (tmm) cc_final: 0.8140 (tmm) REVERT: 0 173 ILE cc_start: 0.8913 (pt) cc_final: 0.8710 (pt) REVERT: 0 220 MET cc_start: 0.7475 (mtp) cc_final: 0.7202 (mtt) REVERT: 0 317 TYR cc_start: 0.9261 (t80) cc_final: 0.8964 (t80) REVERT: 0 327 MET cc_start: 0.8284 (ttt) cc_final: 0.7904 (ttp) REVERT: 1 211 ASP cc_start: 0.8299 (m-30) cc_final: 0.7883 (t70) REVERT: 1 218 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8207 (tm-30) REVERT: 1 225 ASP cc_start: 0.8406 (t70) cc_final: 0.8193 (t0) REVERT: 1 256 MET cc_start: 0.8072 (tmm) cc_final: 0.7694 (tmm) REVERT: 1 261 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8142 (mm-30) REVERT: 1 299 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7860 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1662 time to fit residues: 19.7215 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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** 1 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.063943 restraints weight = 17268.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066201 restraints weight = 9686.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067844 restraints weight = 6431.975| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5722 Z= 0.131 Angle : 0.633 8.397 7712 Z= 0.319 Chirality : 0.045 0.150 860 Planarity : 0.003 0.032 992 Dihedral : 7.108 68.411 754 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.34), residues: 694 helix: 0.14 (0.38), residues: 214 sheet: -1.17 (0.43), residues: 158 loop : -0.84 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 0 296 HIS 0.004 0.001 HIS 1 54 PHE 0.017 0.002 PHE 1 345 TYR 0.014 0.002 TYR 1 4 ARG 0.008 0.001 ARG 1 299 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 202) hydrogen bonds : angle 5.62213 ( 576) covalent geometry : bond 0.00292 ( 5722) covalent geometry : angle 0.63303 ( 7712) *********************** 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 88 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 137 MET cc_start: 0.8740 (tmm) cc_final: 0.8095 (tmm) REVERT: 0 220 MET cc_start: 0.7324 (mtp) cc_final: 0.7063 (mtt) REVERT: 0 236 MET cc_start: 0.9102 (mmm) cc_final: 0.8747 (mmt) REVERT: 0 317 TYR cc_start: 0.9290 (t80) cc_final: 0.9038 (t80) REVERT: 0 327 MET cc_start: 0.8221 (ttt) cc_final: 0.7854 (ttp) REVERT: 1 211 ASP cc_start: 0.8224 (m-30) cc_final: 0.7885 (t70) REVERT: 1 218 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8120 (tm-30) REVERT: 1 225 ASP cc_start: 0.8280 (t70) cc_final: 0.8056 (t0) REVERT: 1 256 MET cc_start: 0.8051 (tmm) cc_final: 0.7657 (tmm) REVERT: 1 261 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8046 (mm-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1559 time to fit residues: 19.1718 Evaluate side-chains 65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** 1 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.074228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.061292 restraints weight = 18147.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063458 restraints weight = 10331.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065026 restraints weight = 6936.052| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5722 Z= 0.231 Angle : 0.714 8.080 7712 Z= 0.360 Chirality : 0.047 0.140 860 Planarity : 0.004 0.030 992 Dihedral : 7.300 68.132 754 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.33), residues: 694 helix: -0.17 (0.36), residues: 226 sheet: -1.22 (0.42), residues: 162 loop : -1.00 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 1 296 HIS 0.005 0.002 HIS 1 54 PHE 0.026 0.002 PHE 1 345 TYR 0.013 0.002 TYR 1 317 ARG 0.005 0.001 ARG 1 85 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 202) hydrogen bonds : angle 5.76705 ( 576) covalent geometry : bond 0.00511 ( 5722) covalent geometry : angle 0.71425 ( 7712) ********************** 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 83 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 137 MET cc_start: 0.8705 (tmm) cc_final: 0.8117 (tmm) REVERT: 0 220 MET cc_start: 0.7326 (mtp) cc_final: 0.6945 (mtt) REVERT: 0 242 ASP cc_start: 0.8982 (m-30) cc_final: 0.8769 (m-30) REVERT: 0 317 TYR cc_start: 0.9263 (t80) cc_final: 0.9000 (t80) REVERT: 0 327 MET cc_start: 0.8258 (ttt) cc_final: 0.7831 (ttp) REVERT: 1 211 ASP cc_start: 0.8309 (m-30) cc_final: 0.7988 (t70) REVERT: 1 218 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8176 (tm-30) REVERT: 1 220 MET cc_start: 0.7424 (mtt) cc_final: 0.7155 (mtt) REVERT: 1 225 ASP cc_start: 0.8411 (t70) cc_final: 0.8201 (t0) REVERT: 1 256 MET cc_start: 0.8081 (tmm) cc_final: 0.7689 (tmm) REVERT: 1 261 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8150 (mm-30) REVERT: 1 348 GLN cc_start: 0.7596 (mm110) cc_final: 0.7151 (mp10) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1628 time to fit residues: 18.3727 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0270 chunk 18 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065179 restraints weight = 17171.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067564 restraints weight = 9582.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069220 restraints weight = 6327.803| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5722 Z= 0.118 Angle : 0.635 7.391 7712 Z= 0.320 Chirality : 0.045 0.153 860 Planarity : 0.004 0.060 992 Dihedral : 6.865 62.129 754 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.34), residues: 694 helix: 0.32 (0.39), residues: 214 sheet: -1.08 (0.42), residues: 162 loop : -0.95 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 0 296 HIS 0.005 0.001 HIS 1 54 PHE 0.013 0.001 PHE 1 345 TYR 0.012 0.001 TYR 1 317 ARG 0.013 0.001 ARG 1 299 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 202) hydrogen bonds : angle 5.58745 ( 576) covalent geometry : bond 0.00256 ( 5722) covalent geometry : angle 0.63481 ( 7712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.59 seconds wall clock time: 31 minutes 44.52 seconds (1904.52 seconds total)