Starting phenix.real_space_refine on Sun Apr 7 08:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dns_27579/04_2024/8dns_27579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dns_27579/04_2024/8dns_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dns_27579/04_2024/8dns_27579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dns_27579/04_2024/8dns_27579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dns_27579/04_2024/8dns_27579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dns_27579/04_2024/8dns_27579.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 4 Chain: "O" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2523 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "P" 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} 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} Chain: "R" 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} Time building chain proxies: 5.47, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 3.71 Conformation dependent library (CDL) restraints added in 1.8 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: 1.16 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: 3.23 Time building geometry restraints manager: 3.98 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: 98.59 - 105.88: 245 105.88 - 113.17: 5533 113.17 - 120.47: 4756 120.47 - 127.76: 3286 127.76 - 135.05: 112 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 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.690 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- 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= 0.430 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 *********************** 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 fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 1.255 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: 0.2476 time to fit residues: 136.5353 Evaluate side-chains 279 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 261 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 0.0770 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 316 ASN O 322 ASN P 53 HIS P 167 ASN P 316 ASN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2525 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= 0.205 Angle : 0.534 6.550 13932 Z= 0.289 Chirality : 0.045 0.166 1580 Planarity : 0.004 0.044 1800 Dihedral : 5.515 32.090 1426 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.87 % Allowed : 14.91 % Favored : 82.22 % 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: 0.33 (0.23), residues: 1324 helix: 1.69 (0.25), residues: 416 sheet: 0.03 (0.28), residues: 276 loop : -0.66 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 313 HIS 0.003 0.001 HIS R 179 PHE 0.013 0.001 PHE Q 286 TYR 0.011 0.001 TYR O 314 ARG 0.005 0.001 ARG Q 323 *********************** 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 295 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 264 time to evaluate : 1.126 Fit side-chains REVERT: O 4 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8347 (p) REVERT: O 5 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7786 (mmtp) REVERT: O 93 GLU cc_start: 0.6870 (tt0) cc_final: 0.6540 (tt0) REVERT: O 133 MET cc_start: 0.7637 (mmm) cc_final: 0.7401 (mmm) REVERT: O 172 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6598 (mt-10) REVERT: P 5 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7905 (mmtp) REVERT: P 172 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6600 (mt-10) REVERT: Q 5 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7881 (mmtp) REVERT: Q 133 MET cc_start: 0.7583 (mmm) cc_final: 0.7360 (mmm) REVERT: Q 172 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6571 (mt-10) REVERT: Q 260 LYS cc_start: 0.7125 (ttmm) cc_final: 0.6924 (tttm) REVERT: R 4 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8351 (p) REVERT: R 24 ASN cc_start: 0.7749 (t0) cc_final: 0.7538 (t0) REVERT: R 93 GLU cc_start: 0.6883 (tt0) cc_final: 0.6562 (tt0) REVERT: R 172 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6511 (mt-10) outliers start: 31 outliers final: 22 residues processed: 282 average time/residue: 0.2389 time to fit residues: 92.8989 Evaluate side-chains 267 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 184 THR Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 308 VAL 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 Q residue 257 ASP Chi-restraints excluded: chain Q residue 308 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 Chi-restraints excluded: chain R residue 257 ASP Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.0170 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 70 ASN O 239 ASN P 53 HIS P 167 ASN P 239 ASN Q 53 HIS Q 167 ASN Q 239 ASN R 53 HIS R 239 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10292 Z= 0.257 Angle : 0.516 5.553 13932 Z= 0.279 Chirality : 0.046 0.171 1580 Planarity : 0.004 0.033 1800 Dihedral : 5.062 31.849 1414 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.59 % Allowed : 17.87 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.22), residues: 1324 helix: 1.56 (0.25), residues: 420 sheet: -0.71 (0.26), residues: 312 loop : -0.73 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS R 137 PHE 0.015 0.001 PHE R 286 TYR 0.009 0.002 TYR O 255 ARG 0.005 0.001 ARG Q 234 *********************** 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 293 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 265 time to evaluate : 1.033 Fit side-chains REVERT: O 172 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6652 (mt-10) REVERT: P 5 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7900 (mmtp) REVERT: P 93 GLU cc_start: 0.6810 (tt0) cc_final: 0.6544 (tt0) REVERT: P 146 ILE cc_start: 0.8339 (mm) cc_final: 0.7987 (mm) REVERT: Q 5 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7869 (mmtp) REVERT: Q 93 GLU cc_start: 0.6860 (tt0) cc_final: 0.6622 (tt0) REVERT: Q 172 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6598 (mt-10) REVERT: Q 260 LYS cc_start: 0.7367 (ttmm) cc_final: 0.7141 (tttm) REVERT: R 24 ASN cc_start: 0.7766 (t0) cc_final: 0.7559 (t0) REVERT: R 172 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6597 (mt-10) REVERT: R 249 LEU cc_start: 0.8138 (mt) cc_final: 0.7773 (mp) outliers start: 28 outliers final: 13 residues processed: 282 average time/residue: 0.2271 time to fit residues: 89.5559 Evaluate side-chains 268 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 255 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 176 THR Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 257 ASP 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 257 ASP Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 257 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.0000 chunk 120 optimal weight: 0.8980 chunk 127 optimal weight: 0.0980 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10292 Z= 0.192 Angle : 0.471 5.680 13932 Z= 0.253 Chirality : 0.044 0.187 1580 Planarity : 0.003 0.033 1800 Dihedral : 4.839 29.555 1411 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.24 % Allowed : 18.80 % Favored : 77.96 % 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: 0.07 (0.23), residues: 1324 helix: 1.56 (0.25), residues: 420 sheet: -0.57 (0.26), residues: 300 loop : -0.65 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.006 0.001 HIS R 137 PHE 0.009 0.001 PHE Q 286 TYR 0.008 0.001 TYR Q 255 ARG 0.006 0.001 ARG O 234 *********************** 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 298 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 1.194 Fit side-chains REVERT: O 50 ASP cc_start: 0.7825 (t0) cc_final: 0.7428 (t0) REVERT: O 334 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7556 (mptt) REVERT: P 5 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7962 (mmtp) REVERT: P 50 ASP cc_start: 0.7861 (t0) cc_final: 0.7414 (t0) REVERT: P 133 MET cc_start: 0.8412 (mmm) cc_final: 0.8025 (mmm) REVERT: P 249 LEU cc_start: 0.8145 (mt) cc_final: 0.7772 (mp) REVERT: Q 5 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7913 (mmtp) REVERT: Q 50 ASP cc_start: 0.7878 (t0) cc_final: 0.7470 (t0) REVERT: Q 172 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6541 (mt-10) REVERT: Q 260 LYS cc_start: 0.7249 (ttmm) cc_final: 0.7044 (tttm) REVERT: R 4 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8520 (p) REVERT: R 24 ASN cc_start: 0.7747 (t0) cc_final: 0.7529 (t0) REVERT: R 50 ASP cc_start: 0.7863 (t0) cc_final: 0.7451 (t0) REVERT: R 93 GLU cc_start: 0.6830 (tt0) cc_final: 0.6607 (tt0) REVERT: R 172 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6565 (mt-10) REVERT: R 249 LEU cc_start: 0.8130 (mt) cc_final: 0.7737 (mp) outliers start: 35 outliers final: 15 residues processed: 285 average time/residue: 0.2310 time to fit residues: 91.9585 Evaluate side-chains 279 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 263 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 257 ASP Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 321 SER Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain Q residue 257 ASP Chi-restraints excluded: chain Q residue 321 SER 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 257 ASP Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10292 Z= 0.373 Angle : 0.555 6.212 13932 Z= 0.298 Chirality : 0.048 0.189 1580 Planarity : 0.004 0.038 1800 Dihedral : 5.168 30.072 1411 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.15 % Allowed : 19.44 % Favored : 77.41 % 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: -0.11 (0.23), residues: 1324 helix: 1.26 (0.25), residues: 420 sheet: -0.75 (0.27), residues: 304 loop : -0.58 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP O 313 HIS 0.004 0.001 HIS Q 179 PHE 0.015 0.002 PHE Q 286 TYR 0.010 0.002 TYR O 314 ARG 0.006 0.001 ARG P 234 *********************** 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 318 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 284 time to evaluate : 1.113 Fit side-chains REVERT: O 105 MET cc_start: 0.7026 (mmm) cc_final: 0.6794 (mmm) REVERT: O 249 LEU cc_start: 0.8303 (mt) cc_final: 0.7923 (mp) REVERT: P 5 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7769 (mmtp) REVERT: Q 5 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7745 (mmtp) REVERT: Q 105 MET cc_start: 0.7085 (mmm) cc_final: 0.5977 (mmm) REVERT: Q 139 LYS cc_start: 0.7340 (mtpp) cc_final: 0.7099 (mtpp) REVERT: Q 172 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6796 (mt-10) REVERT: Q 260 LYS cc_start: 0.7512 (ttmm) cc_final: 0.7275 (tttm) REVERT: R 4 VAL cc_start: 0.8737 (p) cc_final: 0.8367 (p) REVERT: R 24 ASN cc_start: 0.7827 (t0) cc_final: 0.7606 (t0) REVERT: R 93 GLU cc_start: 0.6971 (tt0) cc_final: 0.6742 (tt0) REVERT: R 105 MET cc_start: 0.6883 (mmm) cc_final: 0.6656 (mmm) REVERT: R 172 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6839 (mt-10) outliers start: 34 outliers final: 23 residues processed: 305 average time/residue: 0.2261 time to fit residues: 95.9478 Evaluate side-chains 290 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 267 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 293 SER 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 P residue 257 ASP Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 321 SER 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 257 ASP Chi-restraints excluded: chain Q residue 293 SER Chi-restraints excluded: chain Q residue 321 SER Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 257 ASP Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 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 O 239 ASN O 287 ASN P 239 ASN P 287 ASN R 239 ASN R 287 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10292 Z= 0.253 Angle : 0.510 6.588 13932 Z= 0.271 Chirality : 0.045 0.196 1580 Planarity : 0.003 0.034 1800 Dihedral : 4.952 28.585 1411 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.15 % Allowed : 20.19 % Favored : 76.67 % 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: -0.04 (0.23), residues: 1324 helix: 1.32 (0.26), residues: 420 sheet: -0.89 (0.26), residues: 312 loop : -0.40 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 87 HIS 0.006 0.001 HIS O 137 PHE 0.010 0.001 PHE O 286 TYR 0.009 0.001 TYR O 314 ARG 0.006 0.001 ARG O 234 *********************** 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 313 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 279 time to evaluate : 1.010 Fit side-chains REVERT: O 139 LYS cc_start: 0.7400 (mtpp) cc_final: 0.7146 (mtpp) REVERT: P 5 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7721 (mmtp) REVERT: P 133 MET cc_start: 0.8465 (mmm) cc_final: 0.8128 (mmm) REVERT: Q 5 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7722 (mmtp) REVERT: Q 139 LYS cc_start: 0.7276 (mtpp) cc_final: 0.7062 (mtpp) REVERT: Q 249 LEU cc_start: 0.8312 (mt) cc_final: 0.7958 (mp) REVERT: Q 260 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7310 (tttm) REVERT: R 24 ASN cc_start: 0.7837 (t0) cc_final: 0.7623 (t0) REVERT: R 172 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6695 (mt-10) REVERT: R 249 LEU cc_start: 0.8280 (mt) cc_final: 0.7932 (mp) outliers start: 34 outliers final: 28 residues processed: 298 average time/residue: 0.2377 time to fit residues: 97.0530 Evaluate side-chains 303 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 275 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 57 HIS Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 293 SER 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 P residue 257 ASP Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 321 SER 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 257 ASP Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 293 SER Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 321 SER Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 257 ASP Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 167 ASN Q 167 ASN R 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10292 Z= 0.197 Angle : 0.501 7.001 13932 Z= 0.263 Chirality : 0.045 0.198 1580 Planarity : 0.003 0.033 1800 Dihedral : 4.706 25.267 1410 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.69 % Allowed : 21.20 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1324 helix: 1.27 (0.26), residues: 420 sheet: -0.63 (0.27), residues: 300 loop : -0.35 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 87 HIS 0.004 0.001 HIS O 137 PHE 0.008 0.001 PHE Q 286 TYR 0.007 0.001 TYR P 255 ARG 0.006 0.001 ARG O 234 *********************** 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 306 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 0.880 Fit side-chains REVERT: O 139 LYS cc_start: 0.7373 (mtpp) cc_final: 0.7122 (mtpp) REVERT: P 5 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7731 (mmtp) REVERT: P 133 MET cc_start: 0.8386 (mmm) cc_final: 0.8074 (mmm) REVERT: P 223 GLU cc_start: 0.7291 (tt0) cc_final: 0.7073 (tt0) REVERT: P 249 LEU cc_start: 0.8248 (mt) cc_final: 0.7854 (mp) REVERT: Q 249 LEU cc_start: 0.8277 (mt) cc_final: 0.7880 (mp) REVERT: Q 260 LYS cc_start: 0.7388 (ttmm) cc_final: 0.7148 (tttm) REVERT: R 24 ASN cc_start: 0.7825 (t0) cc_final: 0.7608 (t0) REVERT: R 133 MET cc_start: 0.7981 (mmm) cc_final: 0.7619 (mmm) REVERT: R 249 LEU cc_start: 0.8255 (mt) cc_final: 0.7877 (mp) outliers start: 29 outliers final: 22 residues processed: 293 average time/residue: 0.2621 time to fit residues: 105.4804 Evaluate side-chains 293 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 271 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 198 ASP Chi-restraints excluded: chain O residue 293 SER 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 257 ASP Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 321 SER Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 257 ASP Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 293 SER Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 321 SER Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10292 Z= 0.274 Angle : 0.534 6.712 13932 Z= 0.282 Chirality : 0.047 0.202 1580 Planarity : 0.003 0.037 1800 Dihedral : 4.649 19.748 1408 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 21.02 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1324 helix: 1.20 (0.26), residues: 420 sheet: -0.85 (0.27), residues: 312 loop : -0.33 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 87 HIS 0.004 0.001 HIS R 179 PHE 0.011 0.001 PHE Q 286 TYR 0.009 0.001 TYR O 314 ARG 0.006 0.001 ARG R 234 *********************** 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 306 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 1.184 Fit side-chains REVERT: O 139 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7142 (mtpp) REVERT: P 5 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7759 (mmtp) REVERT: P 61 LYS cc_start: 0.7593 (ttpp) cc_final: 0.7148 (ttpp) REVERT: P 133 MET cc_start: 0.8427 (mmm) cc_final: 0.8201 (mmm) REVERT: P 223 GLU cc_start: 0.7341 (tt0) cc_final: 0.7092 (tt0) REVERT: P 249 LEU cc_start: 0.8340 (mt) cc_final: 0.8002 (mp) REVERT: P 304 ASN cc_start: 0.7785 (m-40) cc_final: 0.7510 (m-40) REVERT: Q 79 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6512 (tp30) REVERT: Q 249 LEU cc_start: 0.8348 (mt) cc_final: 0.7980 (mp) REVERT: Q 260 LYS cc_start: 0.7512 (ttmm) cc_final: 0.7309 (tttm) REVERT: Q 304 ASN cc_start: 0.7842 (m-40) cc_final: 0.7520 (m-40) REVERT: R 24 ASN cc_start: 0.7805 (t0) cc_final: 0.7585 (t0) REVERT: R 133 MET cc_start: 0.8322 (mmm) cc_final: 0.8014 (mmm) REVERT: R 249 LEU cc_start: 0.8321 (mt) cc_final: 0.7999 (mp) REVERT: R 304 ASN cc_start: 0.7827 (m-40) cc_final: 0.7531 (m-40) outliers start: 31 outliers final: 27 residues processed: 291 average time/residue: 0.2315 time to fit residues: 93.0241 Evaluate side-chains 298 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 198 ASP Chi-restraints excluded: chain O residue 293 SER Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 321 SER Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 257 ASP Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 293 SER Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 321 SER 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 257 ASP Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 0.0770 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 304 ASN P 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10292 Z= 0.235 Angle : 0.524 7.254 13932 Z= 0.276 Chirality : 0.046 0.189 1580 Planarity : 0.003 0.033 1800 Dihedral : 4.592 19.999 1408 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.69 % Allowed : 21.67 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.23), residues: 1324 helix: 1.19 (0.26), residues: 420 sheet: -0.85 (0.27), residues: 312 loop : -0.28 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 87 HIS 0.003 0.001 HIS P 179 PHE 0.009 0.001 PHE Q 286 TYR 0.008 0.001 TYR O 314 ARG 0.006 0.001 ARG O 234 *********************** 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 300 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 1.128 Fit side-chains REVERT: P 5 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7754 (mmtp) REVERT: P 133 MET cc_start: 0.8423 (mmm) cc_final: 0.8208 (mmm) REVERT: P 249 LEU cc_start: 0.8312 (mt) cc_final: 0.7968 (mp) REVERT: P 304 ASN cc_start: 0.7850 (m-40) cc_final: 0.7577 (m-40) REVERT: Q 79 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6530 (tp30) REVERT: Q 249 LEU cc_start: 0.8307 (mt) cc_final: 0.7940 (mp) REVERT: Q 260 LYS cc_start: 0.7506 (ttmm) cc_final: 0.7277 (tttm) REVERT: Q 304 ASN cc_start: 0.7846 (m-40) cc_final: 0.7544 (m-40) REVERT: R 24 ASN cc_start: 0.7823 (t0) cc_final: 0.7588 (t0) REVERT: R 249 LEU cc_start: 0.8301 (mt) cc_final: 0.7964 (mp) REVERT: R 304 ASN cc_start: 0.7815 (m-40) cc_final: 0.7525 (m-40) outliers start: 29 outliers final: 28 residues processed: 286 average time/residue: 0.2384 time to fit residues: 93.1859 Evaluate side-chains 297 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 171 VAL Chi-restraints excluded: chain O residue 198 ASP Chi-restraints excluded: chain O residue 257 ASP Chi-restraints excluded: chain O residue 293 SER Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 321 SER Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 257 ASP Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 321 SER Chi-restraints excluded: chain R residue 57 HIS 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 257 ASP Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 111 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4181 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= 0.178 Angle : 0.517 8.252 13932 Z= 0.268 Chirality : 0.045 0.189 1580 Planarity : 0.003 0.033 1800 Dihedral : 4.410 19.407 1408 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.13 % Allowed : 22.31 % 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 (0.23), residues: 1324 helix: 1.24 (0.26), residues: 420 sheet: -0.69 (0.27), residues: 304 loop : -0.29 (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 R 137 PHE 0.006 0.001 PHE Q 286 TYR 0.008 0.001 TYR R 94 ARG 0.007 0.001 ARG Q 234 ********************** 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 288 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 265 time to evaluate : 1.159 Fit side-chains REVERT: P 5 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7760 (mmtp) REVERT: P 133 MET cc_start: 0.8406 (mmm) cc_final: 0.8167 (mmm) REVERT: P 249 LEU cc_start: 0.8196 (mt) cc_final: 0.7800 (mp) REVERT: P 304 ASN cc_start: 0.7849 (m-40) cc_final: 0.7581 (m-40) REVERT: Q 5 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7761 (mmtp) REVERT: Q 249 LEU cc_start: 0.8232 (mt) cc_final: 0.7832 (mp) REVERT: Q 304 ASN cc_start: 0.7856 (m-40) cc_final: 0.7560 (m-40) REVERT: R 24 ASN cc_start: 0.7817 (t0) cc_final: 0.7589 (t0) REVERT: R 249 LEU cc_start: 0.8229 (mt) cc_final: 0.7875 (mp) REVERT: R 304 ASN cc_start: 0.7801 (m-40) cc_final: 0.7548 (m-40) outliers start: 23 outliers final: 22 residues processed: 277 average time/residue: 0.2750 time to fit residues: 103.8083 Evaluate side-chains 282 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 260 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 257 ASP Chi-restraints excluded: chain O residue 293 SER Chi-restraints excluded: chain O residue 308 VAL Chi-restraints excluded: chain O residue 321 SER Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 171 VAL Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 278 GLU Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 321 SER Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain Q residue 257 ASP Chi-restraints excluded: chain Q residue 278 GLU Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain Q residue 321 SER Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 257 ASP Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.134507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.116296 restraints weight = 12262.042| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.67 r_work: 0.3026 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10292 Z= 0.251 Angle : 0.543 7.957 13932 Z= 0.286 Chirality : 0.046 0.190 1580 Planarity : 0.003 0.036 1800 Dihedral : 4.523 19.865 1408 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.50 % Allowed : 22.50 % Favored : 75.00 % 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: 0.02 (0.23), residues: 1324 helix: 1.18 (0.26), residues: 420 sheet: -0.72 (0.28), residues: 304 loop : -0.30 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 87 HIS 0.003 0.001 HIS O 179 PHE 0.010 0.001 PHE Q 286 TYR 0.008 0.001 TYR O 314 ARG 0.007 0.001 ARG O 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.95 seconds wall clock time: 49 minutes 36.20 seconds (2976.20 seconds total)