Starting phenix.real_space_refine on Mon Jul 28 05:38:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dns_27579/07_2025/8dns_27579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dns_27579/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dns_27579/07_2025/8dns_27579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dns_27579/07_2025/8dns_27579.map" model { file = "/net/cci-nas-00/data/ceres_data/8dns_27579/07_2025/8dns_27579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dns_27579/07_2025/8dns_27579.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 1 Chain: "Q" 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, R, O Time building chain proxies: 5.22, per 1000 atoms: 0.52 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: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.21 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: 3.42 Time building geometry restraints manager: 3.42 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: 0.08 Found NCS groups: ncs_group { reference = chain 'Q' selection = chain 'P' selection = chain 'R' selection = chain 'O' } 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: 1.220 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 26.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (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 TRP 0.011 0.002 TRP Q 313 HIS 0.003 0.001 HIS R 137 PHE 0.008 0.001 PHE Q 307 TYR 0.013 0.002 TYR R 314 ARG 0.003 0.001 ARG R 248 Details of bonding type rmsd hydrogen bonds : bond 0.17790 ( 448) hydrogen bonds : angle 8.38270 ( 1224) covalent geometry : bond 0.00648 (10292) covalent geometry : angle 1.46201 (13932) *********************** 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 : 1.147 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: 0.7855 (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: 0.6549 (tt0) REVERT: P 225 ASN cc_start: 0.7847 (t0) cc_final: 0.7627 (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: 0.6689 (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: 0.2321 time to fit residues: 127.9301 Evaluate side-chains 279 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.0270 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.0770 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.141848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.124742 restraints weight = 12266.218| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.71 r_work: 0.3163 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10292 Z= 0.135 Angle : 0.547 6.632 13932 Z= 0.297 Chirality : 0.046 0.167 1580 Planarity : 0.004 0.045 1800 Dihedral : 5.567 31.693 1426 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.13 % Allowed : 14.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1324 helix: 1.65 (0.25), residues: 416 sheet: -0.02 (0.29), residues: 276 loop : -0.67 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 313 HIS 0.004 0.001 HIS R 179 PHE 0.015 0.001 PHE P 286 TYR 0.009 0.002 TYR O 314 ARG 0.006 0.001 ARG Q 323 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 448) hydrogen bonds : angle 6.23969 ( 1224) covalent geometry : bond 0.00309 (10292) covalent geometry : angle 0.54715 (13932) *********************** 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 275 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 1.238 Fit side-chains REVERT: O 4 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8539 (p) REVERT: O 5 LYS cc_start: 0.8556 (mmtt) cc_final: 0.7930 (mmtp) REVERT: O 63 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: O 93 GLU cc_start: 0.7607 (tt0) cc_final: 0.7170 (tt0) REVERT: O 119 VAL cc_start: 0.8987 (t) cc_final: 0.8751 (m) REVERT: O 133 MET cc_start: 0.8096 (mmm) cc_final: 0.7884 (mmm) REVERT: P 5 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8009 (mmtp) REVERT: P 63 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7208 (tm-30) REVERT: P 93 GLU cc_start: 0.7502 (tt0) cc_final: 0.7168 (tt0) REVERT: P 172 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7178 (mt-10) REVERT: P 215 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7898 (mttp) REVERT: Q 5 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8061 (mmtp) REVERT: Q 63 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: Q 93 GLU cc_start: 0.7570 (tt0) cc_final: 0.7245 (tt0) REVERT: Q 119 VAL cc_start: 0.9029 (t) cc_final: 0.8821 (m) REVERT: Q 260 LYS cc_start: 0.7454 (ttmm) cc_final: 0.7137 (tttm) REVERT: R 4 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8535 (p) REVERT: R 93 GLU cc_start: 0.7644 (tt0) cc_final: 0.7191 (tt0) outliers start: 23 outliers final: 13 residues processed: 266 average time/residue: 0.2185 time to fit residues: 81.2960 Evaluate side-chains 250 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 119 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 70 ASN P 53 HIS P 167 ASN P 239 ASN Q 167 ASN R 53 HIS R 167 ASN R 239 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.136963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.119244 restraints weight = 12399.847| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.72 r_work: 0.3063 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10292 Z= 0.145 Angle : 0.513 6.590 13932 Z= 0.278 Chirality : 0.046 0.174 1580 Planarity : 0.004 0.033 1800 Dihedral : 4.997 30.472 1413 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1324 helix: 1.61 (0.25), residues: 420 sheet: -0.46 (0.27), residues: 300 loop : -0.82 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.004 0.001 HIS R 137 PHE 0.015 0.001 PHE P 286 TYR 0.009 0.001 TYR O 255 ARG 0.003 0.001 ARG Q 234 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 448) hydrogen bonds : angle 5.85279 ( 1224) covalent geometry : bond 0.00345 (10292) covalent geometry : angle 0.51282 (13932) *********************** 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 291 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 1.206 Fit side-chains REVERT: O 63 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: O 93 GLU cc_start: 0.7583 (tt0) cc_final: 0.7255 (tt0) REVERT: O 278 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7514 (mt-10) REVERT: P 4 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8418 (p) REVERT: P 5 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8058 (mmtp) REVERT: P 63 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7130 (tm-30) REVERT: P 93 GLU cc_start: 0.7508 (tt0) cc_final: 0.7018 (tt0) REVERT: P 130 MET cc_start: 0.8326 (mtm) cc_final: 0.8063 (mtm) REVERT: P 139 LYS cc_start: 0.7512 (mtpp) cc_final: 0.7228 (mtpp) REVERT: P 145 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7935 (mtmm) REVERT: P 278 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7502 (mt-10) REVERT: Q 4 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8438 (p) REVERT: Q 5 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8060 (mmtp) REVERT: Q 63 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: Q 79 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6238 (tp30) REVERT: Q 93 GLU cc_start: 0.7525 (tt0) cc_final: 0.7070 (tt0) REVERT: Q 145 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7850 (mtmm) REVERT: Q 260 LYS cc_start: 0.7560 (ttmm) cc_final: 0.7202 (tttm) REVERT: R 93 GLU cc_start: 0.7654 (tt0) cc_final: 0.7284 (tt0) REVERT: R 130 MET cc_start: 0.8320 (mtm) cc_final: 0.8038 (mtm) REVERT: R 145 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7926 (mtmm) REVERT: R 249 LEU cc_start: 0.8206 (mt) cc_final: 0.7622 (mt) REVERT: R 278 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7436 (mt-10) outliers start: 27 outliers final: 13 residues processed: 283 average time/residue: 0.2091 time to fit residues: 84.0732 Evaluate side-chains 270 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 4 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 4 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 24 ASN 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 31 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 53 HIS O 239 ASN P 70 ASN Q 53 HIS Q 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.131817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.113839 restraints weight = 12438.072| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.70 r_work: 0.2986 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10292 Z= 0.212 Angle : 0.551 6.958 13932 Z= 0.297 Chirality : 0.048 0.190 1580 Planarity : 0.004 0.031 1800 Dihedral : 5.206 31.792 1411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.50 % Allowed : 18.61 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1324 helix: 1.43 (0.25), residues: 416 sheet: -1.11 (0.26), residues: 312 loop : -0.61 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 313 HIS 0.006 0.001 HIS O 111 PHE 0.017 0.002 PHE P 286 TYR 0.009 0.002 TYR P 255 ARG 0.003 0.001 ARG R 248 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 448) hydrogen bonds : angle 5.89835 ( 1224) covalent geometry : bond 0.00505 (10292) covalent geometry : angle 0.55123 (13932) *********************** 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 301 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.132 Fit side-chains REVERT: O 63 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: O 93 GLU cc_start: 0.7585 (tt0) cc_final: 0.7250 (tt0) REVERT: O 105 MET cc_start: 0.7452 (mmm) cc_final: 0.7063 (mmm) REVERT: O 139 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7299 (mtpp) REVERT: O 249 LEU cc_start: 0.8348 (mt) cc_final: 0.8047 (mp) REVERT: P 5 LYS cc_start: 0.8441 (mmtm) cc_final: 0.7990 (mmtp) REVERT: P 93 GLU cc_start: 0.7568 (tt0) cc_final: 0.7179 (tt0) REVERT: P 139 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7353 (mtpp) REVERT: P 145 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8005 (mtmm) REVERT: Q 5 LYS cc_start: 0.8408 (mmtm) cc_final: 0.7969 (mmtp) REVERT: Q 63 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: Q 79 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6185 (tp30) REVERT: Q 93 GLU cc_start: 0.7585 (tt0) cc_final: 0.7269 (tt0) REVERT: Q 139 LYS cc_start: 0.7531 (mtpp) cc_final: 0.7293 (mtpp) REVERT: Q 145 LYS cc_start: 0.8259 (mtmt) cc_final: 0.8026 (mtmm) REVERT: Q 260 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7507 (tttm) REVERT: R 93 GLU cc_start: 0.7663 (tt0) cc_final: 0.7305 (tt0) REVERT: R 105 MET cc_start: 0.6995 (mpp) cc_final: 0.6527 (mpp) outliers start: 27 outliers final: 14 residues processed: 287 average time/residue: 0.2245 time to fit residues: 89.1710 Evaluate side-chains 269 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 176 THR 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 Q residue 316 ASN Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 176 THR 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 24 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.133052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.115095 restraints weight = 12344.577| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.69 r_work: 0.3008 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10292 Z= 0.158 Angle : 0.508 6.300 13932 Z= 0.274 Chirality : 0.046 0.162 1580 Planarity : 0.003 0.034 1800 Dihedral : 5.010 30.216 1411 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.41 % Allowed : 20.74 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1324 helix: 1.34 (0.25), residues: 420 sheet: -1.30 (0.26), residues: 312 loop : -0.46 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.004 0.001 HIS R 137 PHE 0.012 0.001 PHE Q 286 TYR 0.008 0.001 TYR R 255 ARG 0.006 0.001 ARG O 234 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 448) hydrogen bonds : angle 5.69352 ( 1224) covalent geometry : bond 0.00380 (10292) covalent geometry : angle 0.50810 (13932) *********************** 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: 26 poor density : 262 time to evaluate : 1.240 Fit side-chains REVERT: O 5 LYS cc_start: 0.8338 (mmtm) cc_final: 0.8107 (mmtm) REVERT: O 63 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: O 93 GLU cc_start: 0.7512 (tt0) cc_final: 0.7220 (tt0) REVERT: O 139 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7299 (mtpp) REVERT: O 249 LEU cc_start: 0.8313 (mt) cc_final: 0.8099 (mp) REVERT: P 5 LYS cc_start: 0.8380 (mmtm) cc_final: 0.7960 (mmtp) REVERT: P 93 GLU cc_start: 0.7493 (tt0) cc_final: 0.7128 (tt0) REVERT: P 133 MET cc_start: 0.8585 (mmm) cc_final: 0.8250 (mmm) REVERT: P 139 LYS cc_start: 0.7477 (mtpp) cc_final: 0.7265 (mtpp) REVERT: P 145 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8011 (mtmm) REVERT: P 215 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7864 (mmtm) REVERT: P 249 LEU cc_start: 0.8313 (mt) cc_final: 0.7997 (mp) REVERT: Q 5 LYS cc_start: 0.8375 (mmtm) cc_final: 0.7999 (mmtp) REVERT: Q 79 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6224 (tp30) REVERT: Q 93 GLU cc_start: 0.7578 (tt0) cc_final: 0.7265 (tt0) REVERT: Q 105 MET cc_start: 0.7526 (mmm) cc_final: 0.6571 (mmm) REVERT: Q 133 MET cc_start: 0.8610 (mmm) cc_final: 0.8213 (mmm) REVERT: Q 139 LYS cc_start: 0.7535 (mtpp) cc_final: 0.7279 (mtpp) REVERT: Q 145 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8007 (mtmm) REVERT: Q 249 LEU cc_start: 0.8296 (mt) cc_final: 0.8003 (mp) REVERT: Q 260 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7483 (tttm) REVERT: R 93 GLU cc_start: 0.7600 (tt0) cc_final: 0.7241 (tt0) REVERT: R 249 LEU cc_start: 0.8267 (mt) cc_final: 0.8058 (mp) outliers start: 26 outliers final: 11 residues processed: 281 average time/residue: 0.2365 time to fit residues: 91.8062 Evaluate side-chains 270 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 258 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 176 THR Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain R residue 172 GLU 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 51 optimal weight: 0.1980 chunk 116 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.114311 restraints weight = 12437.390| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.70 r_work: 0.2995 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10292 Z= 0.184 Angle : 0.536 7.322 13932 Z= 0.288 Chirality : 0.047 0.178 1580 Planarity : 0.004 0.038 1800 Dihedral : 5.019 28.616 1411 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.78 % Allowed : 20.83 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1324 helix: 1.30 (0.25), residues: 420 sheet: -1.31 (0.27), residues: 308 loop : -0.44 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 87 HIS 0.003 0.001 HIS P 179 PHE 0.013 0.001 PHE P 286 TYR 0.009 0.001 TYR O 314 ARG 0.006 0.001 ARG R 234 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 448) hydrogen bonds : angle 5.72051 ( 1224) covalent geometry : bond 0.00444 (10292) covalent geometry : angle 0.53562 (13932) *********************** 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 291 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 1.115 Fit side-chains REVERT: O 5 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8105 (mmtm) REVERT: O 63 GLU cc_start: 0.7480 (pp20) cc_final: 0.7213 (tm-30) REVERT: O 93 GLU cc_start: 0.7527 (tt0) cc_final: 0.7199 (tt0) REVERT: O 105 MET cc_start: 0.7373 (mmm) cc_final: 0.7108 (mmm) REVERT: O 139 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7287 (mtpp) REVERT: P 5 LYS cc_start: 0.8302 (mmtm) cc_final: 0.7966 (mmtp) REVERT: P 93 GLU cc_start: 0.7524 (tt0) cc_final: 0.7122 (tt0) REVERT: P 133 MET cc_start: 0.8636 (mmm) cc_final: 0.8386 (mmm) REVERT: P 215 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7859 (mmtm) REVERT: Q 5 LYS cc_start: 0.8307 (mmtm) cc_final: 0.7959 (mmtp) REVERT: Q 79 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6197 (tp30) REVERT: Q 93 GLU cc_start: 0.7598 (tt0) cc_final: 0.7295 (tt0) REVERT: Q 133 MET cc_start: 0.8720 (mmm) cc_final: 0.8451 (mmm) REVERT: Q 139 LYS cc_start: 0.7503 (mtpp) cc_final: 0.7270 (mtpp) REVERT: Q 260 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7511 (tttm) REVERT: Q 304 ASN cc_start: 0.8072 (m-40) cc_final: 0.7708 (m-40) REVERT: Q 305 ASP cc_start: 0.7225 (m-30) cc_final: 0.6929 (t0) REVERT: R 93 GLU cc_start: 0.7609 (tt0) cc_final: 0.7213 (tt0) REVERT: R 105 MET cc_start: 0.7256 (mpp) cc_final: 0.6931 (mpp) REVERT: R 249 LEU cc_start: 0.8387 (mt) cc_final: 0.8129 (mp) REVERT: R 304 ASN cc_start: 0.8084 (m-40) cc_final: 0.7735 (m-40) REVERT: R 305 ASP cc_start: 0.7218 (m-30) cc_final: 0.6905 (t0) outliers start: 30 outliers final: 23 residues processed: 280 average time/residue: 0.2340 time to fit residues: 90.1517 Evaluate side-chains 281 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 98 SER 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 321 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 172 GLU 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 75 THR 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 308 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 176 THR 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 65 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 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 = 0.3328 r_free = 0.3328 target = 0.133170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.114961 restraints weight = 12304.823| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.70 r_work: 0.3003 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10292 Z= 0.161 Angle : 0.529 7.515 13932 Z= 0.281 Chirality : 0.046 0.175 1580 Planarity : 0.004 0.036 1800 Dihedral : 4.903 27.618 1410 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.04 % Allowed : 21.57 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1324 helix: 1.33 (0.26), residues: 420 sheet: -1.35 (0.27), residues: 308 loop : -0.38 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 87 HIS 0.004 0.001 HIS O 137 PHE 0.011 0.001 PHE Q 286 TYR 0.008 0.001 TYR O 314 ARG 0.006 0.001 ARG O 234 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 448) hydrogen bonds : angle 5.63892 ( 1224) covalent geometry : bond 0.00390 (10292) covalent geometry : angle 0.52885 (13932) *********************** 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 272 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.986 Fit side-chains REVERT: O 5 LYS cc_start: 0.8314 (mmtm) cc_final: 0.8111 (mmtm) REVERT: O 63 GLU cc_start: 0.7494 (pp20) cc_final: 0.7225 (tm-30) REVERT: O 93 GLU cc_start: 0.7464 (tt0) cc_final: 0.7124 (tt0) REVERT: O 133 MET cc_start: 0.8605 (mmm) cc_final: 0.8129 (mmm) REVERT: O 249 LEU cc_start: 0.8308 (mt) cc_final: 0.7996 (mp) REVERT: P 4 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8279 (p) REVERT: P 5 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7956 (mmtp) REVERT: P 93 GLU cc_start: 0.7548 (tt0) cc_final: 0.7039 (tt0) REVERT: P 133 MET cc_start: 0.8624 (mmm) cc_final: 0.8406 (mmm) REVERT: P 215 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7823 (mmtm) REVERT: P 223 GLU cc_start: 0.8173 (tt0) cc_final: 0.7859 (tt0) REVERT: P 304 ASN cc_start: 0.8124 (m-40) cc_final: 0.7781 (m-40) REVERT: P 305 ASP cc_start: 0.7353 (m-30) cc_final: 0.7037 (t0) REVERT: Q 5 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7953 (mmtp) REVERT: Q 79 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6197 (tp30) REVERT: Q 93 GLU cc_start: 0.7492 (tt0) cc_final: 0.7219 (tt0) REVERT: Q 105 MET cc_start: 0.7497 (mmm) cc_final: 0.7095 (mmm) REVERT: Q 133 MET cc_start: 0.8632 (mmm) cc_final: 0.8393 (mmm) REVERT: Q 139 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7252 (mtpp) REVERT: Q 249 LEU cc_start: 0.8315 (mt) cc_final: 0.8072 (mp) REVERT: Q 260 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7528 (tttm) REVERT: Q 304 ASN cc_start: 0.8151 (m-40) cc_final: 0.7822 (m-40) REVERT: Q 305 ASP cc_start: 0.7332 (m-30) cc_final: 0.7033 (t0) REVERT: R 93 GLU cc_start: 0.7625 (tt0) cc_final: 0.7246 (tt0) REVERT: R 105 MET cc_start: 0.7239 (mpp) cc_final: 0.6927 (mmm) REVERT: R 133 MET cc_start: 0.8516 (mmm) cc_final: 0.8106 (mmm) REVERT: R 248 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: R 304 ASN cc_start: 0.8161 (m-40) cc_final: 0.7839 (m-40) REVERT: R 305 ASP cc_start: 0.7313 (m-30) cc_final: 0.7050 (t0) outliers start: 22 outliers final: 21 residues processed: 265 average time/residue: 0.2363 time to fit residues: 85.1504 Evaluate side-chains 264 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 130 MET Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 172 GLU Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 243 VAL 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 51 optimal weight: 0.0270 chunk 98 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.3708 ------------------------------------------------------------------------------- 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 R 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.136964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.119146 restraints weight = 12273.559| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.68 r_work: 0.3091 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10292 Z= 0.110 Angle : 0.498 7.215 13932 Z= 0.264 Chirality : 0.045 0.164 1580 Planarity : 0.003 0.030 1800 Dihedral : 4.579 20.098 1408 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.67 % Allowed : 22.31 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1324 helix: 1.43 (0.26), residues: 420 sheet: -1.18 (0.28), residues: 304 loop : -0.34 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 87 HIS 0.003 0.001 HIS P 137 PHE 0.007 0.001 PHE R 286 TYR 0.007 0.001 TYR P 255 ARG 0.007 0.001 ARG O 234 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 448) hydrogen bonds : angle 5.38258 ( 1224) covalent geometry : bond 0.00265 (10292) covalent geometry : angle 0.49837 (13932) *********************** 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 278 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.220 Fit side-chains REVERT: O 5 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8098 (mmtm) REVERT: O 63 GLU cc_start: 0.7433 (pp20) cc_final: 0.7147 (tm-30) REVERT: O 93 GLU cc_start: 0.7334 (tt0) cc_final: 0.6997 (tt0) REVERT: O 133 MET cc_start: 0.8580 (mmm) cc_final: 0.8140 (mmm) REVERT: O 249 LEU cc_start: 0.8195 (mt) cc_final: 0.7849 (mp) REVERT: O 305 ASP cc_start: 0.7571 (m-30) cc_final: 0.7306 (t0) REVERT: P 4 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8215 (p) REVERT: P 5 LYS cc_start: 0.8292 (mmtm) cc_final: 0.7937 (mmtp) REVERT: P 93 GLU cc_start: 0.7319 (tt0) cc_final: 0.6826 (tt0) REVERT: P 133 MET cc_start: 0.8609 (mmm) cc_final: 0.8387 (mmm) REVERT: P 215 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7704 (mmtm) REVERT: P 249 LEU cc_start: 0.8219 (mt) cc_final: 0.7991 (mp) REVERT: P 304 ASN cc_start: 0.8109 (m-40) cc_final: 0.7848 (m-40) REVERT: P 305 ASP cc_start: 0.7272 (m-30) cc_final: 0.7013 (t0) REVERT: Q 4 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8386 (p) REVERT: Q 5 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7945 (mmtp) REVERT: Q 79 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6198 (tp30) REVERT: Q 93 GLU cc_start: 0.7407 (tt0) cc_final: 0.6971 (tt0) REVERT: Q 105 MET cc_start: 0.7420 (mmm) cc_final: 0.7082 (mmm) REVERT: Q 133 MET cc_start: 0.8600 (mmm) cc_final: 0.8362 (mmm) REVERT: Q 249 LEU cc_start: 0.8205 (mt) cc_final: 0.7950 (mp) REVERT: Q 260 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7457 (tttm) REVERT: Q 304 ASN cc_start: 0.8117 (m-40) cc_final: 0.7800 (m-40) REVERT: Q 305 ASP cc_start: 0.7335 (m-30) cc_final: 0.7071 (t0) REVERT: R 93 GLU cc_start: 0.7418 (tt0) cc_final: 0.7060 (tt0) REVERT: R 133 MET cc_start: 0.8538 (mmm) cc_final: 0.8133 (mmm) REVERT: R 249 LEU cc_start: 0.8239 (mt) cc_final: 0.7993 (mp) REVERT: R 305 ASP cc_start: 0.7299 (m-30) cc_final: 0.7064 (t0) outliers start: 18 outliers final: 13 residues processed: 271 average time/residue: 0.2506 time to fit residues: 92.5690 Evaluate side-chains 264 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 130 MET 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 172 GLU Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 243 VAL 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 121 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 ASN R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.134517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.116308 restraints weight = 12382.431| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.71 r_work: 0.3054 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4102 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= 0.151 Angle : 0.533 7.644 13932 Z= 0.284 Chirality : 0.047 0.188 1580 Planarity : 0.004 0.039 1800 Dihedral : 4.641 20.679 1408 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.30 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1324 helix: 1.26 (0.26), residues: 420 sheet: -1.14 (0.29), residues: 296 loop : -0.36 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 87 HIS 0.003 0.001 HIS Q 179 PHE 0.011 0.001 PHE O 286 TYR 0.008 0.001 TYR O 314 ARG 0.008 0.001 ARG Q 323 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 448) hydrogen bonds : angle 5.49362 ( 1224) covalent geometry : bond 0.00368 (10292) covalent geometry : angle 0.53254 (13932) *********************** 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 254 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 1.248 Fit side-chains REVERT: O 5 LYS cc_start: 0.8329 (mmtm) cc_final: 0.8125 (mmtm) REVERT: O 63 GLU cc_start: 0.7439 (pp20) cc_final: 0.7165 (tm-30) REVERT: O 93 GLU cc_start: 0.7414 (tt0) cc_final: 0.7064 (tt0) REVERT: O 133 MET cc_start: 0.8656 (mmm) cc_final: 0.8314 (mmm) REVERT: O 249 LEU cc_start: 0.8239 (mt) cc_final: 0.7927 (mp) REVERT: O 305 ASP cc_start: 0.7626 (m-30) cc_final: 0.7347 (t0) REVERT: P 4 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8238 (p) REVERT: P 5 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7948 (mmtp) REVERT: P 61 LYS cc_start: 0.7996 (ttpp) cc_final: 0.7489 (ttpp) REVERT: P 93 GLU cc_start: 0.7303 (tt0) cc_final: 0.6822 (tt0) REVERT: P 215 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7730 (mmtm) REVERT: P 304 ASN cc_start: 0.8195 (m-40) cc_final: 0.7888 (m-40) REVERT: P 305 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7101 (t0) REVERT: Q 5 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7963 (mmtp) REVERT: Q 79 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6154 (tp30) REVERT: Q 93 GLU cc_start: 0.7423 (tt0) cc_final: 0.7148 (tt0) REVERT: Q 105 MET cc_start: 0.7441 (mmm) cc_final: 0.7095 (mmm) REVERT: Q 260 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7466 (tttm) REVERT: Q 304 ASN cc_start: 0.8236 (m-40) cc_final: 0.7919 (m-40) REVERT: Q 305 ASP cc_start: 0.7424 (m-30) cc_final: 0.7157 (t0) REVERT: R 93 GLU cc_start: 0.7439 (tt0) cc_final: 0.7054 (tt0) REVERT: R 133 MET cc_start: 0.8610 (mmm) cc_final: 0.8285 (mmm) REVERT: R 305 ASP cc_start: 0.7390 (m-30) cc_final: 0.7148 (t0) outliers start: 14 outliers final: 12 residues processed: 247 average time/residue: 0.2527 time to fit residues: 84.1110 Evaluate side-chains 255 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain Q residue 172 GLU Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN R 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.136801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.118613 restraints weight = 12407.633| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.72 r_work: 0.3076 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10292 Z= 0.121 Angle : 0.528 7.749 13932 Z= 0.278 Chirality : 0.046 0.170 1580 Planarity : 0.003 0.033 1800 Dihedral : 4.570 19.971 1408 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.30 % Allowed : 23.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1324 helix: 1.27 (0.26), residues: 420 sheet: -1.16 (0.28), residues: 304 loop : -0.27 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 87 HIS 0.004 0.001 HIS P 137 PHE 0.008 0.001 PHE P 286 TYR 0.007 0.001 TYR P 255 ARG 0.007 0.001 ARG O 234 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 448) hydrogen bonds : angle 5.40023 ( 1224) covalent geometry : bond 0.00293 (10292) covalent geometry : angle 0.52823 (13932) ********************** 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: 14 poor density : 238 time to evaluate : 1.169 Fit side-chains REVERT: O 5 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8147 (mmtm) REVERT: O 63 GLU cc_start: 0.7453 (pp20) cc_final: 0.7176 (tm-30) REVERT: O 93 GLU cc_start: 0.7351 (tt0) cc_final: 0.7015 (tt0) REVERT: O 133 MET cc_start: 0.8584 (mmm) cc_final: 0.8233 (mmm) REVERT: O 249 LEU cc_start: 0.8167 (mt) cc_final: 0.7875 (mp) REVERT: O 305 ASP cc_start: 0.7618 (m-30) cc_final: 0.7339 (t0) REVERT: P 4 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8192 (p) REVERT: P 5 LYS cc_start: 0.8332 (mmtm) cc_final: 0.7967 (mmtp) REVERT: P 93 GLU cc_start: 0.7303 (tt0) cc_final: 0.6807 (tt0) REVERT: P 215 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7715 (mmtm) REVERT: P 249 LEU cc_start: 0.8191 (mt) cc_final: 0.7977 (mp) REVERT: P 304 ASN cc_start: 0.8242 (m-40) cc_final: 0.7954 (m-40) REVERT: P 305 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7154 (t0) REVERT: Q 4 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8359 (p) REVERT: Q 5 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7980 (mmtp) REVERT: Q 79 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6162 (tp30) REVERT: Q 93 GLU cc_start: 0.7428 (tt0) cc_final: 0.6993 (tt0) REVERT: Q 105 MET cc_start: 0.7440 (mmm) cc_final: 0.7071 (mmm) REVERT: Q 249 LEU cc_start: 0.8198 (mt) cc_final: 0.7952 (mp) REVERT: Q 260 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7439 (tttm) REVERT: Q 304 ASN cc_start: 0.8250 (m-40) cc_final: 0.7937 (m-40) REVERT: Q 305 ASP cc_start: 0.7460 (m-30) cc_final: 0.7153 (t0) REVERT: R 93 GLU cc_start: 0.7383 (tt0) cc_final: 0.7015 (tt0) REVERT: R 133 MET cc_start: 0.8626 (mmm) cc_final: 0.8292 (mmm) REVERT: R 249 LEU cc_start: 0.8168 (mt) cc_final: 0.7932 (mp) REVERT: R 305 ASP cc_start: 0.7495 (m-30) cc_final: 0.7220 (t0) outliers start: 14 outliers final: 11 residues processed: 246 average time/residue: 0.2530 time to fit residues: 83.6823 Evaluate side-chains 242 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 172 GLU Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 172 GLU Chi-restraints excluded: chain R residue 243 VAL 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 59 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.135309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.116995 restraints weight = 12309.701| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.71 r_work: 0.3055 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10292 Z= 0.146 Angle : 0.542 7.951 13932 Z= 0.286 Chirality : 0.046 0.175 1580 Planarity : 0.004 0.038 1800 Dihedral : 4.598 20.353 1408 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.30 % Allowed : 23.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1324 helix: 1.23 (0.26), residues: 420 sheet: -1.08 (0.29), residues: 296 loop : -0.33 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 87 HIS 0.004 0.001 HIS P 137 PHE 0.011 0.001 PHE O 286 TYR 0.007 0.001 TYR P 255 ARG 0.007 0.001 ARG P 323 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 448) hydrogen bonds : angle 5.48754 ( 1224) covalent geometry : bond 0.00355 (10292) covalent geometry : angle 0.54178 (13932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5342.01 seconds wall clock time: 93 minutes 25.01 seconds (5605.01 seconds total)