Starting phenix.real_space_refine on Sat Aug 23 05:42:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dns_27579/08_2025/8dns_27579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dns_27579/08_2025/8dns_27579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dns_27579/08_2025/8dns_27579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dns_27579/08_2025/8dns_27579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dns_27579/08_2025/8dns_27579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dns_27579/08_2025/8dns_27579.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.068 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6384 2.51 5 N 1752 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 1 Chain: "O" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2523 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Restraints were copied for chains: P, Q, R Time building chain proxies: 2.07, per 1000 atoms: 0.21 Number of scatterers: 10092 At special positions: 0 Unit cell: (90.95, 99.51, 86.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1908 8.00 N 1752 7.00 C 6384 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: 1.03 Conformation dependent library (CDL) restraints added in 419.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 35.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'O' and resid 12 through 26 Processing helix chain 'O' and resid 39 through 48 Processing helix chain 'O' and resid 104 through 115 removed outlier: 4.229A pdb=" N HIS O 111 " --> pdb=" O LYS O 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU O 112 " --> pdb=" O ALA O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 Processing helix chain 'O' and resid 151 through 168 Proline residue: O 159 - end of helix Processing helix chain 'O' and resid 195 through 200 removed outlier: 3.700A pdb=" N GLY O 199 " --> pdb=" O LEU O 195 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG O 200 " --> pdb=" O TRP O 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 195 through 200' Processing helix chain 'O' and resid 212 through 221 removed outlier: 3.623A pdb=" N LYS O 219 " --> pdb=" O LYS O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 254 through 268 Processing helix chain 'O' and resid 282 through 287 Processing helix chain 'O' and resid 316 through 335 removed outlier: 3.634A pdb=" N TYR O 320 " --> pdb=" O ASN O 316 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER O 321 " --> pdb=" O GLU O 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 26 Processing helix chain 'P' and resid 39 through 48 Processing helix chain 'P' and resid 104 through 115 removed outlier: 4.228A pdb=" N HIS P 111 " --> pdb=" O LYS P 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU P 112 " --> pdb=" O ALA P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 151 through 168 Proline residue: P 159 - end of helix Processing helix chain 'P' and resid 195 through 200 removed outlier: 3.700A pdb=" N GLY P 199 " --> pdb=" O LEU P 195 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG P 200 " --> pdb=" O TRP P 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 195 through 200' Processing helix chain 'P' and resid 212 through 221 removed outlier: 3.624A pdb=" N LYS P 219 " --> pdb=" O LYS P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 268 Processing helix chain 'P' and resid 282 through 287 Processing helix chain 'P' and resid 316 through 335 removed outlier: 3.633A pdb=" N TYR P 320 " --> pdb=" O ASN P 316 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER P 321 " --> pdb=" O GLU P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 26 Processing helix chain 'Q' and resid 39 through 48 Processing helix chain 'Q' and resid 104 through 115 removed outlier: 4.229A pdb=" N HIS Q 111 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 Processing helix chain 'Q' and resid 151 through 168 Proline residue: Q 159 - end of helix Processing helix chain 'Q' and resid 195 through 200 removed outlier: 3.701A pdb=" N GLY Q 199 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG Q 200 " --> pdb=" O TRP Q 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 195 through 200' Processing helix chain 'Q' and resid 212 through 221 removed outlier: 3.624A pdb=" N LYS Q 219 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 268 Processing helix chain 'Q' and resid 282 through 287 Processing helix chain 'Q' and resid 316 through 335 removed outlier: 3.633A pdb=" N TYR Q 320 " --> pdb=" O ASN Q 316 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER Q 321 " --> pdb=" O GLU Q 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 26 Processing helix chain 'R' and resid 39 through 48 Processing helix chain 'R' and resid 104 through 115 removed outlier: 4.229A pdb=" N HIS R 111 " --> pdb=" O LYS R 107 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU R 112 " --> pdb=" O ALA R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 151 through 168 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 195 through 200 removed outlier: 3.700A pdb=" N GLY R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG R 200 " --> pdb=" O TRP R 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 195 through 200' Processing helix chain 'R' and resid 212 through 221 removed outlier: 3.623A pdb=" N LYS R 219 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 268 Processing helix chain 'R' and resid 282 through 287 Processing helix chain 'R' and resid 316 through 335 removed outlier: 3.633A pdb=" N TYR R 320 " --> pdb=" O ASN R 316 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER R 321 " --> pdb=" O GLU R 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 60 through 63 removed outlier: 5.902A pdb=" N VAL O 31 " --> pdb=" O PRO O 73 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL O 6 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA O 32 " --> pdb=" O VAL O 6 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL O 95 " --> pdb=" O ILE O 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 49 through 50 Processing sheet with id=AA3, first strand: chain 'O' and resid 207 through 209 removed outlier: 9.349A pdb=" N THR O 229 " --> pdb=" O VAL O 171 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY O 173 " --> pdb=" O THR O 229 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N MET O 231 " --> pdb=" O GLY O 173 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET O 175 " --> pdb=" O MET O 231 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE O 233 " --> pdb=" O MET O 175 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR O 177 " --> pdb=" O PHE O 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU O 172 " --> pdb=" O ARG O 248 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE O 311 " --> pdb=" O ASP O 296 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY O 275 " --> pdb=" O PHE O 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 60 through 63 removed outlier: 5.902A pdb=" N VAL P 31 " --> pdb=" O PRO P 73 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL P 6 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA P 32 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL P 95 " --> pdb=" O ILE P 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'P' and resid 207 through 209 removed outlier: 9.349A pdb=" N THR P 229 " --> pdb=" O VAL P 171 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY P 173 " --> pdb=" O THR P 229 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N MET P 231 " --> pdb=" O GLY P 173 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET P 175 " --> pdb=" O MET P 231 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE P 233 " --> pdb=" O MET P 175 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR P 177 " --> pdb=" O PHE P 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU P 172 " --> pdb=" O ARG P 248 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE P 311 " --> pdb=" O ASP P 296 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY P 275 " --> pdb=" O PHE P 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 60 through 63 removed outlier: 5.903A pdb=" N VAL Q 31 " --> pdb=" O PRO Q 73 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL Q 6 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA Q 32 " --> pdb=" O VAL Q 6 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL Q 95 " --> pdb=" O ILE Q 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 49 through 50 Processing sheet with id=AA9, first strand: chain 'Q' and resid 207 through 209 removed outlier: 9.350A pdb=" N THR Q 229 " --> pdb=" O VAL Q 171 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY Q 173 " --> pdb=" O THR Q 229 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N MET Q 231 " --> pdb=" O GLY Q 173 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET Q 175 " --> pdb=" O MET Q 231 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE Q 233 " --> pdb=" O MET Q 175 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR Q 177 " --> pdb=" O PHE Q 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU Q 172 " --> pdb=" O ARG Q 248 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE Q 311 " --> pdb=" O ASP Q 296 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY Q 275 " --> pdb=" O PHE Q 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 60 through 63 removed outlier: 5.902A pdb=" N VAL R 31 " --> pdb=" O PRO R 73 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL R 6 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA R 32 " --> pdb=" O VAL R 6 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL R 95 " --> pdb=" O ILE R 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 49 through 50 Processing sheet with id=AB3, first strand: chain 'R' and resid 207 through 209 removed outlier: 9.348A pdb=" N THR R 229 " --> pdb=" O VAL R 171 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY R 173 " --> pdb=" O THR R 229 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N MET R 231 " --> pdb=" O GLY R 173 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET R 175 " --> pdb=" O MET R 231 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE R 233 " --> pdb=" O MET R 175 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR R 177 " --> pdb=" O PHE R 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU R 172 " --> pdb=" O ARG R 248 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE R 311 " --> pdb=" O ASP R 296 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY R 275 " --> pdb=" O PHE R 295 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1224 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: 1.75 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3048 1.33 - 1.45: 1336 1.45 - 1.57: 5824 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10292 Sorted by residual: bond pdb=" C ASP Q 35 " pdb=" O ASP Q 35 " ideal model delta sigma weight residual 1.249 1.223 0.026 8.50e-03 1.38e+04 9.08e+00 bond pdb=" C ASP O 35 " pdb=" O ASP O 35 " ideal model delta sigma weight residual 1.249 1.223 0.026 8.50e-03 1.38e+04 9.02e+00 bond pdb=" C ASP P 35 " pdb=" O ASP P 35 " ideal model delta sigma weight residual 1.249 1.223 0.025 8.50e-03 1.38e+04 8.92e+00 bond pdb=" C ASP R 35 " pdb=" O ASP R 35 " ideal model delta sigma weight residual 1.249 1.223 0.025 8.50e-03 1.38e+04 8.92e+00 bond pdb=" C ASP R 81 " pdb=" N PRO R 82 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.25e-02 6.40e+03 6.55e+00 ... (remaining 10287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 12614 2.21 - 4.43: 1010 4.43 - 6.64: 220 6.64 - 8.85: 56 8.85 - 11.07: 32 Bond angle restraints: 13932 Sorted by residual: angle pdb=" N ILE Q 207 " pdb=" CA ILE Q 207 " pdb=" C ILE Q 207 " ideal model delta sigma weight residual 107.55 118.48 -10.93 9.90e-01 1.02e+00 1.22e+02 angle pdb=" N ILE P 207 " pdb=" CA ILE P 207 " pdb=" C ILE P 207 " ideal model delta sigma weight residual 107.55 118.47 -10.92 9.90e-01 1.02e+00 1.22e+02 angle pdb=" N ILE O 207 " pdb=" CA ILE O 207 " pdb=" C ILE O 207 " ideal model delta sigma weight residual 107.55 118.46 -10.91 9.90e-01 1.02e+00 1.21e+02 angle pdb=" N ILE R 207 " pdb=" CA ILE R 207 " pdb=" C ILE R 207 " ideal model delta sigma weight residual 107.55 118.44 -10.89 9.90e-01 1.02e+00 1.21e+02 angle pdb=" N ALA R 238 " pdb=" CA ALA R 238 " pdb=" C ALA R 238 " ideal model delta sigma weight residual 111.36 122.03 -10.67 1.09e+00 8.42e-01 9.57e+01 ... (remaining 13927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.11: 5347 11.11 - 22.23: 529 22.23 - 33.34: 175 33.34 - 44.45: 49 44.45 - 55.56: 20 Dihedral angle restraints: 6120 sinusoidal: 2348 harmonic: 3772 Sorted by residual: dihedral pdb=" C VAL R 220 " pdb=" N VAL R 220 " pdb=" CA VAL R 220 " pdb=" CB VAL R 220 " ideal model delta harmonic sigma weight residual -122.00 -129.34 7.34 0 2.50e+00 1.60e-01 8.62e+00 dihedral pdb=" C VAL O 220 " pdb=" N VAL O 220 " pdb=" CA VAL O 220 " pdb=" CB VAL O 220 " ideal model delta harmonic sigma weight residual -122.00 -129.33 7.33 0 2.50e+00 1.60e-01 8.59e+00 dihedral pdb=" C VAL P 220 " pdb=" N VAL P 220 " pdb=" CA VAL P 220 " pdb=" CB VAL P 220 " ideal model delta harmonic sigma weight residual -122.00 -129.31 7.31 0 2.50e+00 1.60e-01 8.56e+00 ... (remaining 6117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1006 0.070 - 0.140: 379 0.140 - 0.210: 143 0.210 - 0.281: 38 0.281 - 0.351: 14 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA ALA P 238 " pdb=" N ALA P 238 " pdb=" C ALA P 238 " pdb=" CB ALA P 238 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ALA Q 238 " pdb=" N ALA Q 238 " pdb=" C ALA Q 238 " pdb=" CB ALA Q 238 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ALA R 238 " pdb=" N ALA R 238 " pdb=" C ALA R 238 " pdb=" CB ALA R 238 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1577 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 158 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO R 159 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA O 158 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO O 159 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO O 159 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO O 159 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Q 158 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO Q 159 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO Q 159 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Q 159 " 0.035 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 4401 2.92 - 3.41: 9808 3.41 - 3.91: 18463 3.91 - 4.40: 21463 4.40 - 4.90: 34527 Nonbonded interactions: 88662 Sorted by model distance: nonbonded pdb=" O GLN O 185 " pdb=" CG2 THR R 187 " model vdw 2.425 3.460 nonbonded pdb=" O GLN P 185 " pdb=" CG2 THR Q 187 " model vdw 2.425 3.460 nonbonded pdb=" CG2 THR P 187 " pdb=" O GLN Q 185 " model vdw 2.428 3.460 nonbonded pdb=" CG2 THR O 187 " pdb=" O GLN R 185 " model vdw 2.447 3.460 nonbonded pdb=" OH TYR O 45 " pdb=" O GLN Q 280 " model vdw 2.450 3.040 ... (remaining 88657 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.910 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 10292 Z= 0.489 Angle : 1.462 11.066 13932 Z= 1.020 Chirality : 0.091 0.351 1580 Planarity : 0.005 0.060 1800 Dihedral : 11.073 55.564 3712 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.33 % Allowed : 7.78 % Favored : 88.89 % 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 aren not related in a simple way. whole: -0.08 (0.23), residues: 1324 helix: 0.94 (0.26), residues: 412 sheet: 0.05 (0.32), residues: 260 loop : -0.70 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 248 TYR 0.013 0.002 TYR R 314 PHE 0.008 0.001 PHE Q 307 TRP 0.011 0.002 TRP Q 313 HIS 0.003 0.001 HIS R 137 Details of bonding type rmsd covalent geometry : bond 0.00648 (10292) covalent geometry : angle 1.46201 (13932) hydrogen bonds : bond 0.17790 ( 448) hydrogen bonds : angle 8.38270 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 365 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: O 4 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8148 (p) REVERT: O 93 GLU cc_start: 0.6993 (tt0) cc_final: 0.6792 (tt0) REVERT: O 168 PHE cc_start: 0.8203 (m-80) cc_final: 0.7846 (m-10) REVERT: P 4 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8259 (p) REVERT: P 5 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8065 (mmtp) REVERT: P 93 GLU cc_start: 0.6780 (tt0) cc_final: 0.6548 (tt0) REVERT: P 225 ASN cc_start: 0.7847 (t0) cc_final: 0.7628 (t0) REVERT: P 287 ASN cc_start: 0.8223 (t0) cc_final: 0.7997 (t0) REVERT: Q 4 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8254 (p) REVERT: Q 5 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8016 (mmtp) REVERT: Q 93 GLU cc_start: 0.6878 (tt0) cc_final: 0.6633 (tt0) REVERT: Q 260 LYS cc_start: 0.6918 (ttmm) cc_final: 0.6690 (tttm) REVERT: R 4 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8156 (p) REVERT: R 93 GLU cc_start: 0.6876 (tt0) cc_final: 0.6659 (tt0) REVERT: R 287 ASN cc_start: 0.8233 (t0) cc_final: 0.8006 (t0) outliers start: 36 outliers final: 14 residues processed: 397 average time/residue: 0.1048 time to fit residues: 58.3654 Evaluate side-chains 278 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 294 THR Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 294 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 53 HIS O 316 ASN O 322 ASN O 330 HIS P 53 HIS P 167 ASN P 316 ASN P 330 HIS Q 53 HIS Q 72 ASN Q 167 ASN Q 316 ASN Q 322 ASN R 53 HIS R 167 ASN R 225 ASN R 316 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.144824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.127610 restraints weight = 12244.364| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.78 r_work: 0.3135 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10292 Z= 0.131 Angle : 0.543 6.340 13932 Z= 0.295 Chirality : 0.046 0.169 1580 Planarity : 0.004 0.045 1800 Dihedral : 5.555 31.885 1426 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.22 % Allowed : 14.81 % Favored : 82.96 % 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 aren not related in a simple way. whole: 0.29 (0.23), residues: 1324 helix: 1.66 (0.25), residues: 416 sheet: -0.01 (0.29), residues: 276 loop : -0.68 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 323 TYR 0.010 0.002 TYR O 314 PHE 0.014 0.001 PHE P 286 TRP 0.007 0.001 TRP O 313 HIS 0.005 0.001 HIS O 137 Details of bonding type rmsd covalent geometry : bond 0.00301 (10292) covalent geometry : angle 0.54295 (13932) hydrogen bonds : bond 0.03866 ( 448) hydrogen bonds : angle 6.25322 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.395 Fit side-chains REVERT: O 4 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8555 (p) REVERT: O 5 LYS cc_start: 0.8507 (mmtt) cc_final: 0.7945 (mmtp) REVERT: O 63 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: O 93 GLU cc_start: 0.7660 (tt0) cc_final: 0.7229 (tt0) REVERT: O 119 VAL cc_start: 0.8994 (t) cc_final: 0.8755 (m) REVERT: O 133 MET cc_start: 0.8060 (mmm) cc_final: 0.7854 (mmm) REVERT: P 4 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8476 (p) REVERT: P 5 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8030 (mmtp) REVERT: P 63 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7206 (tm-30) REVERT: P 93 GLU cc_start: 0.7558 (tt0) cc_final: 0.7095 (tt0) REVERT: P 119 VAL cc_start: 0.9023 (t) cc_final: 0.8822 (m) REVERT: P 172 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7201 (mt-10) REVERT: P 215 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7902 (mttp) REVERT: Q 5 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8079 (mmtp) REVERT: Q 63 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: Q 93 GLU cc_start: 0.7625 (tt0) cc_final: 0.7297 (tt0) REVERT: Q 119 VAL cc_start: 0.9009 (t) cc_final: 0.8793 (m) REVERT: Q 260 LYS cc_start: 0.7486 (ttmm) cc_final: 0.7149 (tttm) REVERT: R 4 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8542 (p) REVERT: R 93 GLU cc_start: 0.7683 (tt0) cc_final: 0.7227 (tt0) outliers start: 24 outliers final: 13 residues processed: 270 average time/residue: 0.1036 time to fit residues: 39.4051 Evaluate side-chains 252 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 294 THR Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 53 HIS O 70 ASN O 239 ASN P 53 HIS P 167 ASN P 239 ASN Q 53 HIS Q 167 ASN Q 239 ASN R 53 HIS R 167 ASN R 239 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.132308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.114342 restraints weight = 12616.652| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.71 r_work: 0.2992 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10292 Z= 0.223 Angle : 0.572 6.740 13932 Z= 0.312 Chirality : 0.048 0.177 1580 Planarity : 0.004 0.035 1800 Dihedral : 5.310 33.787 1414 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.31 % Allowed : 18.15 % Favored : 79.54 % 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 aren not related in a simple way. whole: -0.17 (0.23), residues: 1324 helix: 1.43 (0.25), residues: 416 sheet: -0.79 (0.27), residues: 312 loop : -0.79 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 16 TYR 0.009 0.002 TYR O 255 PHE 0.021 0.002 PHE O 286 TRP 0.010 0.002 TRP Q 313 HIS 0.004 0.001 HIS Q 111 Details of bonding type rmsd covalent geometry : bond 0.00534 (10292) covalent geometry : angle 0.57247 (13932) hydrogen bonds : bond 0.04295 ( 448) hydrogen bonds : angle 6.12924 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 0.348 Fit side-chains REVERT: O 63 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: O 93 GLU cc_start: 0.7649 (tt0) cc_final: 0.7314 (tt0) REVERT: O 131 PHE cc_start: 0.8041 (m-80) cc_final: 0.7754 (m-80) REVERT: O 249 LEU cc_start: 0.8261 (mt) cc_final: 0.7797 (mp) REVERT: O 278 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7618 (mt-10) REVERT: O 318 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8076 (t80) REVERT: P 5 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8035 (mmtp) REVERT: P 63 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7136 (tm-30) REVERT: P 93 GLU cc_start: 0.7536 (tt0) cc_final: 0.7158 (tt0) REVERT: P 139 LYS cc_start: 0.7575 (mtpp) cc_final: 0.7289 (mtpp) REVERT: P 249 LEU cc_start: 0.8294 (mt) cc_final: 0.8042 (mp) REVERT: Q 5 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8044 (mmtp) REVERT: Q 63 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: Q 79 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6200 (tp30) REVERT: Q 93 GLU cc_start: 0.7648 (tt0) cc_final: 0.7311 (tt0) REVERT: Q 131 PHE cc_start: 0.7993 (m-80) cc_final: 0.7605 (m-80) REVERT: Q 139 LYS cc_start: 0.7530 (mtpp) cc_final: 0.7265 (mtpp) REVERT: Q 249 LEU cc_start: 0.8325 (mt) cc_final: 0.8084 (mp) REVERT: Q 260 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7420 (tttm) REVERT: R 93 GLU cc_start: 0.7690 (tt0) cc_final: 0.7335 (tt0) REVERT: R 145 LYS cc_start: 0.8259 (mtmt) cc_final: 0.8005 (mtmm) REVERT: R 249 LEU cc_start: 0.8305 (mt) cc_final: 0.8075 (mp) outliers start: 25 outliers final: 13 residues processed: 285 average time/residue: 0.0933 time to fit residues: 37.5600 Evaluate side-chains 274 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 70 ASN P 167 ASN Q 167 ASN R 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.133068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.115050 restraints weight = 12525.235| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.72 r_work: 0.3003 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10292 Z= 0.164 Angle : 0.514 6.524 13932 Z= 0.277 Chirality : 0.046 0.176 1580 Planarity : 0.004 0.035 1800 Dihedral : 5.117 32.964 1411 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.87 % Allowed : 19.63 % Favored : 77.50 % 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 aren not related in a simple way. whole: -0.18 (0.23), residues: 1324 helix: 1.42 (0.25), residues: 416 sheet: -1.06 (0.26), residues: 312 loop : -0.59 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 234 TYR 0.009 0.001 TYR O 255 PHE 0.013 0.001 PHE P 286 TRP 0.004 0.001 TRP Q 313 HIS 0.004 0.001 HIS R 137 Details of bonding type rmsd covalent geometry : bond 0.00393 (10292) covalent geometry : angle 0.51365 (13932) hydrogen bonds : bond 0.03583 ( 448) hydrogen bonds : angle 5.81443 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.409 Fit side-chains REVERT: O 5 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8105 (mmtm) REVERT: O 63 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: O 93 GLU cc_start: 0.7555 (tt0) cc_final: 0.7227 (tt0) REVERT: O 105 MET cc_start: 0.7456 (mmm) cc_final: 0.7082 (mmm) REVERT: O 139 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7293 (mtpp) REVERT: O 249 LEU cc_start: 0.8326 (mt) cc_final: 0.8088 (mp) REVERT: O 278 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7640 (mt-10) REVERT: O 318 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8047 (t80) REVERT: P 5 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7975 (mmtp) REVERT: P 93 GLU cc_start: 0.7556 (tt0) cc_final: 0.7166 (tt0) REVERT: P 112 LEU cc_start: 0.8306 (mm) cc_final: 0.8103 (mm) REVERT: P 133 MET cc_start: 0.8568 (mmm) cc_final: 0.8207 (mmm) REVERT: P 139 LYS cc_start: 0.7535 (mtpp) cc_final: 0.7320 (mtpp) REVERT: P 249 LEU cc_start: 0.8333 (mt) cc_final: 0.8109 (mp) REVERT: Q 5 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8001 (mmtp) REVERT: Q 79 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6195 (tp30) REVERT: Q 93 GLU cc_start: 0.7570 (tt0) cc_final: 0.7265 (tt0) REVERT: Q 112 LEU cc_start: 0.8306 (mm) cc_final: 0.8092 (mm) REVERT: Q 139 LYS cc_start: 0.7502 (mtpp) cc_final: 0.7243 (mtpp) REVERT: Q 172 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: Q 249 LEU cc_start: 0.8339 (mt) cc_final: 0.8129 (mp) REVERT: Q 260 LYS cc_start: 0.7831 (ttmm) cc_final: 0.7446 (tttm) REVERT: R 93 GLU cc_start: 0.7611 (tt0) cc_final: 0.7251 (tt0) REVERT: R 105 MET cc_start: 0.7377 (mpp) cc_final: 0.6573 (mpp) REVERT: R 249 LEU cc_start: 0.8329 (mt) cc_final: 0.8125 (mp) outliers start: 31 outliers final: 17 residues processed: 277 average time/residue: 0.0913 time to fit residues: 35.5131 Evaluate side-chains 266 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 172 GLU Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 223 GLU Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.132847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.115031 restraints weight = 12438.548| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.69 r_work: 0.3006 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10292 Z= 0.164 Angle : 0.513 6.455 13932 Z= 0.275 Chirality : 0.046 0.177 1580 Planarity : 0.004 0.034 1800 Dihedral : 5.017 30.127 1411 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % 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 aren not related in a simple way. whole: -0.21 (0.23), residues: 1324 helix: 1.38 (0.25), residues: 416 sheet: -1.25 (0.27), residues: 312 loop : -0.50 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 234 TYR 0.008 0.001 TYR P 255 PHE 0.013 0.001 PHE O 286 TRP 0.004 0.001 TRP P 87 HIS 0.003 0.001 HIS Q 137 Details of bonding type rmsd covalent geometry : bond 0.00398 (10292) covalent geometry : angle 0.51277 (13932) hydrogen bonds : bond 0.03450 ( 448) hydrogen bonds : angle 5.73322 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.253 Fit side-chains REVERT: O 5 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8125 (mmtm) REVERT: O 63 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: O 93 GLU cc_start: 0.7558 (tt0) cc_final: 0.7243 (tt0) REVERT: O 105 MET cc_start: 0.7452 (mmm) cc_final: 0.6471 (mmm) REVERT: O 127 ASP cc_start: 0.7516 (p0) cc_final: 0.7111 (p0) REVERT: O 139 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7278 (mtpp) REVERT: O 318 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (t80) REVERT: P 5 LYS cc_start: 0.8374 (mmtm) cc_final: 0.7962 (mmtp) REVERT: P 93 GLU cc_start: 0.7556 (tt0) cc_final: 0.7158 (tt0) REVERT: P 139 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7256 (mtpp) REVERT: Q 5 LYS cc_start: 0.8382 (mmtm) cc_final: 0.7952 (mmtp) REVERT: Q 79 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6174 (tp30) REVERT: Q 93 GLU cc_start: 0.7578 (tt0) cc_final: 0.7261 (tt0) REVERT: Q 249 LEU cc_start: 0.8353 (mt) cc_final: 0.8139 (mp) REVERT: Q 260 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7489 (tttm) REVERT: R 93 GLU cc_start: 0.7618 (tt0) cc_final: 0.7253 (tt0) REVERT: R 105 MET cc_start: 0.7272 (mpp) cc_final: 0.7018 (mmm) REVERT: R 166 ASP cc_start: 0.7293 (m-30) cc_final: 0.7073 (m-30) outliers start: 30 outliers final: 17 residues processed: 278 average time/residue: 0.0899 time to fit residues: 34.7765 Evaluate side-chains 275 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.0370 chunk 120 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.134879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.116845 restraints weight = 12424.768| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.70 r_work: 0.3046 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10292 Z= 0.132 Angle : 0.502 6.620 13932 Z= 0.267 Chirality : 0.045 0.165 1580 Planarity : 0.003 0.034 1800 Dihedral : 4.876 26.925 1411 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.85 % Allowed : 20.83 % Favored : 77.31 % 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 aren not related in a simple way. whole: -0.12 (0.23), residues: 1324 helix: 1.39 (0.26), residues: 420 sheet: -1.29 (0.27), residues: 316 loop : -0.32 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 234 TYR 0.008 0.001 TYR O 314 PHE 0.010 0.001 PHE Q 286 TRP 0.004 0.001 TRP P 87 HIS 0.003 0.001 HIS Q 179 Details of bonding type rmsd covalent geometry : bond 0.00319 (10292) covalent geometry : angle 0.50183 (13932) hydrogen bonds : bond 0.03137 ( 448) hydrogen bonds : angle 5.52866 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.408 Fit side-chains REVERT: O 5 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8094 (mmtm) REVERT: O 63 GLU cc_start: 0.7389 (pp20) cc_final: 0.7132 (tm-30) REVERT: O 93 GLU cc_start: 0.7399 (tt0) cc_final: 0.7085 (tt0) REVERT: O 105 MET cc_start: 0.7470 (mmm) cc_final: 0.6339 (mmm) REVERT: O 139 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7343 (mtpp) REVERT: O 318 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8073 (t80) REVERT: P 5 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7972 (mmtp) REVERT: P 93 GLU cc_start: 0.7488 (tt0) cc_final: 0.7097 (tt0) REVERT: P 133 MET cc_start: 0.8526 (mmm) cc_final: 0.8151 (mmm) REVERT: P 139 LYS cc_start: 0.7537 (mtpp) cc_final: 0.7318 (mtpp) REVERT: P 215 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7868 (mmtm) REVERT: P 223 GLU cc_start: 0.8125 (tt0) cc_final: 0.7886 (tt0) REVERT: P 323 ARG cc_start: 0.8644 (mmp80) cc_final: 0.8428 (mmp80) REVERT: Q 4 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8443 (p) REVERT: Q 5 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7977 (mmtp) REVERT: Q 79 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6185 (tp30) REVERT: Q 93 GLU cc_start: 0.7452 (tt0) cc_final: 0.7046 (tt0) REVERT: Q 105 MET cc_start: 0.7543 (mmm) cc_final: 0.7328 (mmm) REVERT: Q 133 MET cc_start: 0.8472 (mmm) cc_final: 0.7953 (mmm) REVERT: Q 260 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7452 (tttm) REVERT: Q 305 ASP cc_start: 0.7162 (m-30) cc_final: 0.6856 (t0) REVERT: R 93 GLU cc_start: 0.7547 (tt0) cc_final: 0.7186 (tt0) REVERT: R 105 MET cc_start: 0.7173 (mpp) cc_final: 0.6879 (mmm) REVERT: R 166 ASP cc_start: 0.7523 (m-30) cc_final: 0.7317 (m-30) REVERT: R 249 LEU cc_start: 0.8233 (mt) cc_final: 0.8004 (mp) REVERT: R 323 ARG cc_start: 0.8652 (mmp80) cc_final: 0.8441 (mmp80) outliers start: 20 outliers final: 15 residues processed: 267 average time/residue: 0.1086 time to fit residues: 39.8177 Evaluate side-chains 265 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 172 GLU Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 ASN Q 239 ASN R 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.133871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.115576 restraints weight = 12310.980| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.71 r_work: 0.3041 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10292 Z= 0.150 Angle : 0.516 6.807 13932 Z= 0.275 Chirality : 0.046 0.172 1580 Planarity : 0.003 0.037 1800 Dihedral : 4.699 20.629 1408 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.31 % Allowed : 20.93 % Favored : 76.76 % 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 aren not related in a simple way. whole: -0.13 (0.23), residues: 1324 helix: 1.33 (0.26), residues: 420 sheet: -1.23 (0.28), residues: 308 loop : -0.35 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 234 TYR 0.008 0.001 TYR O 314 PHE 0.011 0.001 PHE R 286 TRP 0.004 0.001 TRP P 87 HIS 0.003 0.001 HIS Q 179 Details of bonding type rmsd covalent geometry : bond 0.00363 (10292) covalent geometry : angle 0.51619 (13932) hydrogen bonds : bond 0.03234 ( 448) hydrogen bonds : angle 5.50871 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.306 Fit side-chains REVERT: O 5 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8114 (mmtm) REVERT: O 63 GLU cc_start: 0.7408 (pp20) cc_final: 0.7136 (tm-30) REVERT: O 93 GLU cc_start: 0.7441 (tt0) cc_final: 0.7108 (tt0) REVERT: O 139 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7314 (mtpp) REVERT: O 318 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8074 (t80) REVERT: P 5 LYS cc_start: 0.8331 (mmtm) cc_final: 0.7982 (mmtp) REVERT: P 93 GLU cc_start: 0.7485 (tt0) cc_final: 0.7107 (tt0) REVERT: P 133 MET cc_start: 0.8609 (mmm) cc_final: 0.8295 (mmm) REVERT: P 139 LYS cc_start: 0.7534 (mtpp) cc_final: 0.7294 (mtpp) REVERT: P 215 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7834 (mmtm) REVERT: P 223 GLU cc_start: 0.8084 (tt0) cc_final: 0.7866 (tt0) REVERT: P 304 ASN cc_start: 0.8133 (m-40) cc_final: 0.7812 (m-40) REVERT: Q 4 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8433 (p) REVERT: Q 5 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7965 (mmtp) REVERT: Q 79 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6204 (tp30) REVERT: Q 93 GLU cc_start: 0.7428 (tt0) cc_final: 0.7016 (tt0) REVERT: Q 133 MET cc_start: 0.8637 (mmm) cc_final: 0.8230 (mmm) REVERT: Q 248 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7935 (ttp-110) REVERT: Q 260 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7476 (tttm) REVERT: Q 304 ASN cc_start: 0.8122 (m-40) cc_final: 0.7764 (m-40) REVERT: R 93 GLU cc_start: 0.7551 (tt0) cc_final: 0.7183 (tt0) REVERT: R 105 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6567 (mmm) REVERT: R 133 MET cc_start: 0.8327 (mmm) cc_final: 0.8005 (mmm) REVERT: R 166 ASP cc_start: 0.7569 (m-30) cc_final: 0.7342 (m-30) REVERT: R 249 LEU cc_start: 0.8313 (mt) cc_final: 0.8072 (mp) REVERT: R 304 ASN cc_start: 0.8103 (m-40) cc_final: 0.7770 (m-40) REVERT: R 305 ASP cc_start: 0.7344 (m-30) cc_final: 0.7035 (t0) outliers start: 25 outliers final: 18 residues processed: 266 average time/residue: 0.1071 time to fit residues: 38.6519 Evaluate side-chains 266 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 172 GLU Chi-restraints excluded: chain Q residue 305 ASP Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 105 MET Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN O 304 ASN P 167 ASN R 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.133445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.115148 restraints weight = 12363.172| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.71 r_work: 0.3031 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10292 Z= 0.171 Angle : 0.533 6.617 13932 Z= 0.285 Chirality : 0.047 0.188 1580 Planarity : 0.004 0.038 1800 Dihedral : 4.740 20.531 1408 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.04 % Allowed : 21.48 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.24), residues: 1324 helix: 1.32 (0.26), residues: 420 sheet: -1.24 (0.28), residues: 308 loop : -0.35 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 248 TYR 0.010 0.001 TYR O 314 PHE 0.012 0.001 PHE Q 286 TRP 0.004 0.001 TRP R 87 HIS 0.005 0.001 HIS O 137 Details of bonding type rmsd covalent geometry : bond 0.00411 (10292) covalent geometry : angle 0.53263 (13932) hydrogen bonds : bond 0.03363 ( 448) hydrogen bonds : angle 5.59527 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 0.421 Fit side-chains REVERT: O 5 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8120 (mmtm) REVERT: O 63 GLU cc_start: 0.7421 (pp20) cc_final: 0.7140 (tm-30) REVERT: O 93 GLU cc_start: 0.7516 (tt0) cc_final: 0.7173 (tt0) REVERT: O 305 ASP cc_start: 0.7757 (m-30) cc_final: 0.7514 (t0) REVERT: O 318 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8090 (t80) REVERT: P 5 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7970 (mmtp) REVERT: P 93 GLU cc_start: 0.7495 (tt0) cc_final: 0.7103 (tt0) REVERT: P 133 MET cc_start: 0.8622 (mmm) cc_final: 0.8350 (mmm) REVERT: P 215 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7882 (mmtm) REVERT: P 223 GLU cc_start: 0.8141 (tt0) cc_final: 0.7885 (tt0) REVERT: P 304 ASN cc_start: 0.8220 (m-40) cc_final: 0.7902 (m-40) REVERT: P 318 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8261 (t80) REVERT: Q 4 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8445 (p) REVERT: Q 5 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7963 (mmtp) REVERT: Q 93 GLU cc_start: 0.7439 (tt0) cc_final: 0.7039 (tt0) REVERT: Q 105 MET cc_start: 0.7510 (mmm) cc_final: 0.7259 (mmm) REVERT: Q 133 MET cc_start: 0.8568 (mmm) cc_final: 0.8260 (mmm) REVERT: Q 260 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7472 (tttm) REVERT: Q 304 ASN cc_start: 0.8210 (m-40) cc_final: 0.7880 (m-40) REVERT: R 93 GLU cc_start: 0.7539 (tt0) cc_final: 0.7174 (tt0) REVERT: R 133 MET cc_start: 0.8530 (mmm) cc_final: 0.8233 (mmm) REVERT: R 147 ILE cc_start: 0.8433 (tt) cc_final: 0.8012 (tt) REVERT: R 166 ASP cc_start: 0.7391 (m-30) cc_final: 0.7189 (m-30) REVERT: R 304 ASN cc_start: 0.8233 (m-40) cc_final: 0.7930 (m-40) REVERT: R 305 ASP cc_start: 0.7398 (m-30) cc_final: 0.7127 (t0) outliers start: 22 outliers final: 16 residues processed: 253 average time/residue: 0.1176 time to fit residues: 40.6159 Evaluate side-chains 257 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 239 ASN Q 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.133488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.115014 restraints weight = 12279.656| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.71 r_work: 0.3031 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10292 Z= 0.176 Angle : 0.547 7.080 13932 Z= 0.291 Chirality : 0.047 0.179 1580 Planarity : 0.004 0.038 1800 Dihedral : 4.773 20.572 1408 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.94 % Allowed : 22.22 % Favored : 75.83 % 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 aren not related in a simple way. whole: -0.16 (0.24), residues: 1324 helix: 1.26 (0.26), residues: 420 sheet: -1.23 (0.29), residues: 308 loop : -0.34 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 323 TYR 0.010 0.001 TYR O 314 PHE 0.012 0.001 PHE O 286 TRP 0.005 0.001 TRP R 87 HIS 0.004 0.001 HIS R 179 Details of bonding type rmsd covalent geometry : bond 0.00425 (10292) covalent geometry : angle 0.54673 (13932) hydrogen bonds : bond 0.03399 ( 448) hydrogen bonds : angle 5.62844 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.260 Fit side-chains REVERT: O 5 LYS cc_start: 0.8350 (mmtm) cc_final: 0.8129 (mmtm) REVERT: O 63 GLU cc_start: 0.7465 (pp20) cc_final: 0.7193 (tm-30) REVERT: O 93 GLU cc_start: 0.7449 (tt0) cc_final: 0.7094 (tt0) REVERT: O 305 ASP cc_start: 0.7809 (m-30) cc_final: 0.7566 (t0) REVERT: O 318 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8124 (t80) REVERT: P 5 LYS cc_start: 0.8339 (mmtm) cc_final: 0.7969 (mmtp) REVERT: P 93 GLU cc_start: 0.7486 (tt0) cc_final: 0.7088 (tt0) REVERT: P 133 MET cc_start: 0.8665 (mmm) cc_final: 0.8452 (mmm) REVERT: P 215 LYS cc_start: 0.8365 (mmtt) cc_final: 0.7885 (mmtm) REVERT: P 304 ASN cc_start: 0.8234 (m-40) cc_final: 0.7939 (m-40) REVERT: P 305 ASP cc_start: 0.7616 (m-30) cc_final: 0.7337 (t0) REVERT: P 318 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8286 (t80) REVERT: Q 4 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8405 (p) REVERT: Q 5 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7951 (mmtp) REVERT: Q 93 GLU cc_start: 0.7436 (tt0) cc_final: 0.7011 (tt0) REVERT: Q 105 MET cc_start: 0.7468 (mmm) cc_final: 0.7178 (mmm) REVERT: Q 133 MET cc_start: 0.8637 (mmm) cc_final: 0.8376 (mmm) REVERT: Q 260 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7524 (tttm) REVERT: Q 304 ASN cc_start: 0.8246 (m-40) cc_final: 0.7942 (m-40) REVERT: Q 318 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8174 (t80) REVERT: R 93 GLU cc_start: 0.7561 (tt0) cc_final: 0.7173 (tt0) REVERT: R 147 ILE cc_start: 0.8412 (tt) cc_final: 0.8007 (tt) REVERT: R 166 ASP cc_start: 0.7483 (m-30) cc_final: 0.7265 (m-30) REVERT: R 304 ASN cc_start: 0.8205 (m-40) cc_final: 0.7954 (m-40) outliers start: 21 outliers final: 16 residues processed: 254 average time/residue: 0.1008 time to fit residues: 34.8823 Evaluate side-chains 257 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 318 PHE Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN P 167 ASN Q 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.133873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.115355 restraints weight = 12205.207| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.72 r_work: 0.3044 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10292 Z= 0.162 Angle : 0.541 7.867 13932 Z= 0.287 Chirality : 0.046 0.180 1580 Planarity : 0.004 0.038 1800 Dihedral : 4.748 20.571 1408 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.94 % Allowed : 22.50 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.24), residues: 1324 helix: 1.25 (0.26), residues: 420 sheet: -1.20 (0.29), residues: 308 loop : -0.31 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 323 TYR 0.009 0.001 TYR O 314 PHE 0.011 0.001 PHE O 286 TRP 0.005 0.001 TRP P 87 HIS 0.003 0.001 HIS Q 179 Details of bonding type rmsd covalent geometry : bond 0.00391 (10292) covalent geometry : angle 0.54066 (13932) hydrogen bonds : bond 0.03293 ( 448) hydrogen bonds : angle 5.58105 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.316 Fit side-chains REVERT: O 5 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8138 (mmtm) REVERT: O 63 GLU cc_start: 0.7474 (pp20) cc_final: 0.7207 (tm-30) REVERT: O 93 GLU cc_start: 0.7430 (tt0) cc_final: 0.7079 (tt0) REVERT: O 257 ASP cc_start: 0.7783 (m-30) cc_final: 0.7564 (m-30) REVERT: O 305 ASP cc_start: 0.7813 (m-30) cc_final: 0.7574 (t0) REVERT: O 318 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8107 (t80) REVERT: P 5 LYS cc_start: 0.8344 (mmtm) cc_final: 0.7970 (mmtp) REVERT: P 61 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7581 (ttpp) REVERT: P 93 GLU cc_start: 0.7390 (tt0) cc_final: 0.6986 (tt0) REVERT: P 133 MET cc_start: 0.8637 (mmm) cc_final: 0.8392 (mmm) REVERT: P 215 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7859 (mmtm) REVERT: P 304 ASN cc_start: 0.8243 (m-40) cc_final: 0.7942 (m-40) REVERT: P 305 ASP cc_start: 0.7658 (m-30) cc_final: 0.7388 (t0) REVERT: P 318 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8277 (t80) REVERT: Q 4 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8430 (p) REVERT: Q 5 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7940 (mmtp) REVERT: Q 93 GLU cc_start: 0.7461 (tt0) cc_final: 0.7049 (tt0) REVERT: Q 105 MET cc_start: 0.7497 (mmm) cc_final: 0.7211 (mmm) REVERT: Q 133 MET cc_start: 0.8625 (mmm) cc_final: 0.8385 (mmm) REVERT: Q 260 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7497 (tttm) REVERT: Q 304 ASN cc_start: 0.8272 (m-40) cc_final: 0.7976 (m-40) REVERT: Q 305 ASP cc_start: 0.7776 (m-30) cc_final: 0.7502 (t0) REVERT: Q 318 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8160 (t80) REVERT: R 93 GLU cc_start: 0.7552 (tt0) cc_final: 0.7170 (tt0) REVERT: R 133 MET cc_start: 0.8691 (mmm) cc_final: 0.8322 (mmm) REVERT: R 147 ILE cc_start: 0.8262 (tt) cc_final: 0.7818 (tt) REVERT: R 166 ASP cc_start: 0.7485 (m-30) cc_final: 0.7269 (m-30) REVERT: R 304 ASN cc_start: 0.8201 (m-40) cc_final: 0.7954 (m-40) REVERT: R 318 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8229 (t80) outliers start: 21 outliers final: 16 residues processed: 247 average time/residue: 0.0946 time to fit residues: 32.2372 Evaluate side-chains 251 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 318 PHE Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 318 PHE Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 318 PHE Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.115898 restraints weight = 12293.089| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.72 r_work: 0.3054 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10292 Z= 0.157 Angle : 0.538 7.290 13932 Z= 0.286 Chirality : 0.046 0.179 1580 Planarity : 0.004 0.037 1800 Dihedral : 4.731 20.605 1408 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.13 % Allowed : 22.59 % Favored : 75.28 % 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 aren not related in a simple way. whole: -0.11 (0.24), residues: 1324 helix: 1.23 (0.26), residues: 420 sheet: -1.15 (0.29), residues: 308 loop : -0.27 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 323 TYR 0.009 0.001 TYR O 314 PHE 0.011 0.001 PHE O 286 TRP 0.005 0.001 TRP R 87 HIS 0.003 0.001 HIS R 179 Details of bonding type rmsd covalent geometry : bond 0.00380 (10292) covalent geometry : angle 0.53765 (13932) hydrogen bonds : bond 0.03276 ( 448) hydrogen bonds : angle 5.57536 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.60 seconds wall clock time: 38 minutes 4.12 seconds (2284.12 seconds total)