Starting phenix.real_space_refine on Thu Jul 2 10:32:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffn_31569/07_2026/7ffn_31569_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffn_31569/07_2026/7ffn_31569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_2026/7ffn_31569_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_2026/7ffn_31569_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_2026/7ffn_31569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_2026/7ffn_31569.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 5434 2.51 5 N 1470 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "M" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.70, per 1000 atoms: 0.20 Number of scatterers: 8589 At special positions: 0 Unit cell: (150.48, 96.36, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 1617 8.00 N 1470 7.00 C 5434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 42 " distance=2.03 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 55 " distance=1.09 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 64 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 312.7 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 31 sheets defined 17.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.802A pdb=" N ARG K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.785A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 48 No H-bonds generated for 'chain 'M' and resid 46 through 48' Processing helix chain 'M' and resid 55 through 59 removed outlier: 3.973A pdb=" N SER M 59 " --> pdb=" O PHE M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.805A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.515A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.616A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.502A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.572A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.900A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 439 Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.658A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.705A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE K 214 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 229 through 230 removed outlier: 3.866A pdb=" N ALA K 239 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'M' and resid 34 through 36 Processing sheet with id=AA9, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 35 through 37 removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 35 through 37 removed outlier: 5.834A pdb=" N TYR N 98 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N SER N 51 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS N 96 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N TYR N 53 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ASP N 94 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AB4, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AB5, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AB6, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.714A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.684A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AB9, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AC1, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AC2, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AC3, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.369A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN O 134 " --> pdb=" O PRO O 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS O 35 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 46 through 48 removed outlier: 3.640A pdb=" N TYR O 46 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 51 through 55 removed outlier: 3.715A pdb=" N ALA O 59 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AC7, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.889A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AC9, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AD2, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.012A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AD4, first strand: chain 'O' and resid 364 through 369 316 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2743 1.34 - 1.46: 2134 1.46 - 1.59: 3844 1.59 - 1.71: 2 1.71 - 1.84: 88 Bond restraints: 8811 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.089 1.08e-02 8.57e+03 6.74e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.310 -0.076 1.21e-02 6.83e+03 3.90e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.89e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.22e-02 6.72e+03 2.81e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.505 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 11827 3.18 - 6.35: 142 6.35 - 9.53: 19 9.53 - 12.71: 2 12.71 - 15.88: 2 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.32 -15.88 1.93e+00 2.68e-01 6.77e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.04 -7.27 1.25e+00 6.40e-01 3.39e+01 angle pdb=" N VAL N 179 " pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 109.80 117.18 -7.38 1.33e+00 5.65e-01 3.08e+01 angle pdb=" C VAL N 174 " pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 122.47 129.59 -7.12 1.50e+00 4.44e-01 2.25e+01 angle pdb=" C CYS N 22 " pdb=" N ALA N 23 " pdb=" CA ALA N 23 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5089 17.61 - 35.22: 174 35.22 - 52.82: 37 52.82 - 70.43: 5 70.43 - 88.04: 6 Dihedral angle restraints: 5311 sinusoidal: 2086 harmonic: 3225 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 27 " pdb=" CB CYS N 27 " ideal model delta sinusoidal sigma weight residual 93.00 173.64 -80.64 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA ILE O 369 " pdb=" C ILE O 369 " pdb=" N CYS O 370 " pdb=" CA CYS O 370 " ideal model delta harmonic sigma weight residual 180.00 -135.79 -44.21 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CB CYS M 37 " pdb=" SG CYS M 37 " pdb=" SG CYS M 55 " pdb=" CB CYS M 55 " ideal model delta sinusoidal sigma weight residual 93.00 14.07 78.93 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1081 0.072 - 0.144: 218 0.144 - 0.215: 27 0.215 - 0.287: 1 0.287 - 0.359: 2 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA ASP N 175 " pdb=" N ASP N 175 " pdb=" C ASP N 175 " pdb=" CB ASP N 175 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASP M 57 " pdb=" N ASP M 57 " pdb=" C ASP M 57 " pdb=" CB ASP M 57 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA HIS N 156 " pdb=" N HIS N 156 " pdb=" C HIS N 156 " pdb=" CB HIS N 156 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1326 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 13 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO N 14 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 88 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO N 89 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO N 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 89 " 0.038 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 34 2.52 - 3.11: 5668 3.11 - 3.71: 12191 3.71 - 4.30: 17289 4.30 - 4.90: 29700 Nonbonded interactions: 64882 Sorted by model distance: nonbonded pdb=" OH TYR K 173 " pdb=" NE2 GLN O 439 " model vdw 1.924 3.120 nonbonded pdb=" O ASN O 442 " pdb=" ND2 ASN O 442 " model vdw 2.111 3.120 nonbonded pdb=" OH TYR N 359 " pdb=" O ALA O 401 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU O 120 " pdb=" OH TYR O 122 " model vdw 2.276 3.040 nonbonded pdb=" O GLY O 182 " pdb=" OG1 THR O 263 " model vdw 2.312 3.040 ... (remaining 64877 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.950 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.012 0.938 8827 Z= 0.601 Angle : 1.008 26.552 12024 Z= 0.546 Chirality : 0.058 0.359 1329 Planarity : 0.008 0.099 1549 Dihedral : 9.733 88.037 3197 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 0.53 % Allowed : 2.76 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.21), residues: 1102 helix: -1.89 (0.34), residues: 134 sheet: -1.32 (0.26), residues: 347 loop : -2.48 (0.20), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 230 TYR 0.031 0.003 TYR O 308 PHE 0.023 0.003 PHE N 328 TRP 0.022 0.003 TRP M 47 HIS 0.011 0.002 HIS N 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.34 ( 8811) covalent geometry : angle 0.94538 / 0.52 (11992) SS BOND : bond 0.23452 / 11.73 ( 16) SS BOND : angle 6.85804 / 3.89 ( 32) hydrogen bonds : bond 0.21044 / 14.05 ( 298) hydrogen bonds : angle 8.76345 / 6.02 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.294 Fit side-chains REVERT: K 166 LYS cc_start: 0.6128 (tttt) cc_final: 0.5681 (pttt) REVERT: K 232 ASP cc_start: 0.1805 (p0) cc_final: 0.1476 (p0) REVERT: N 9 TYR cc_start: 0.8310 (m-80) cc_final: 0.8040 (m-80) REVERT: N 365 MET cc_start: 0.7551 (ttt) cc_final: 0.7237 (pmt) REVERT: N 398 THR cc_start: 0.8150 (m) cc_final: 0.7610 (t) REVERT: O 13 ILE cc_start: 0.9253 (mt) cc_final: 0.9043 (mm) REVERT: O 115 LEU cc_start: 0.8498 (tm) cc_final: 0.8134 (tp) REVERT: O 281 ASP cc_start: 0.7805 (t0) cc_final: 0.7575 (t0) REVERT: O 409 TRP cc_start: 0.8455 (m100) cc_final: 0.8235 (m100) REVERT: O 442 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5851 (t0) outliers start: 5 outliers final: 1 residues processed: 208 average time/residue: 0.4741 time to fit residues: 105.2786 Evaluate side-chains 110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN K 211 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS N 159 GLN N 160 ASN N 225 GLN N 353 HIS O 66 GLN O 102 GLN O 125 HIS O 157 ASN O 264 ASN O 360 ASN O 392 GLN O 394 HIS O 442 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111519 restraints weight = 11118.453| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.67 r_work: 0.3077 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8827 Z= 0.123 Angle : 0.592 8.520 12024 Z= 0.309 Chirality : 0.044 0.164 1329 Planarity : 0.006 0.083 1549 Dihedral : 5.519 48.561 1207 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.19 % Allowed : 10.84 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.24), residues: 1102 helix: 0.32 (0.45), residues: 134 sheet: -0.65 (0.27), residues: 356 loop : -1.80 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 175 TYR 0.018 0.001 TYR O 308 PHE 0.013 0.001 PHE N 328 TRP 0.010 0.001 TRP K 202 HIS 0.004 0.001 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8811) covalent geometry : angle 0.58698 / 0.31 (11992) SS BOND : bond 0.00659 / 0.42 ( 16) SS BOND : angle 1.53760 / 1.32 ( 32) hydrogen bonds : bond 0.03273 / 2.12 ( 298) hydrogen bonds : angle 5.58143 / 3.81 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.203 Fit side-chains REVERT: K 166 LYS cc_start: 0.7476 (tttt) cc_final: 0.7242 (pttt) REVERT: K 190 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7878 (mtpt) REVERT: K 209 TYR cc_start: 0.8443 (t80) cc_final: 0.7891 (t80) REVERT: M 36 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8337 (ttp) REVERT: N 9 TYR cc_start: 0.8395 (m-80) cc_final: 0.8070 (m-80) REVERT: N 21 ARG cc_start: 0.7956 (mmt90) cc_final: 0.5707 (mmm-85) REVERT: N 42 ASP cc_start: 0.8235 (m-30) cc_final: 0.7988 (m-30) REVERT: N 66 MET cc_start: 0.9425 (ttt) cc_final: 0.9152 (ttt) REVERT: N 76 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: N 88 ARG cc_start: 0.8474 (mtm110) cc_final: 0.6553 (mtt180) REVERT: N 113 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: N 173 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7287 (mm-30) REVERT: N 290 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8051 (tttm) REVERT: N 365 MET cc_start: 0.8492 (ttt) cc_final: 0.7530 (pmt) REVERT: N 398 THR cc_start: 0.8574 (m) cc_final: 0.8220 (p) REVERT: O 13 ILE cc_start: 0.9270 (mt) cc_final: 0.9056 (mm) REVERT: O 24 TYR cc_start: 0.8478 (m-80) cc_final: 0.8214 (m-80) REVERT: O 115 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8515 (tp) REVERT: O 175 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7603 (ttp-110) REVERT: O 281 ASP cc_start: 0.8392 (t0) cc_final: 0.8134 (t0) REVERT: O 409 TRP cc_start: 0.8523 (m100) cc_final: 0.8129 (m100) outliers start: 30 outliers final: 10 residues processed: 161 average time/residue: 0.4695 time to fit residues: 80.8047 Evaluate side-chains 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 190 LYS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 0.2980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN K 211 ASN N 152 GLN N 159 GLN N 358 HIS O 102 GLN O 130 GLN O 155 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106609 restraints weight = 10966.210| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.60 r_work: 0.3019 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8827 Z= 0.139 Angle : 0.603 12.728 12024 Z= 0.311 Chirality : 0.045 0.244 1329 Planarity : 0.006 0.074 1549 Dihedral : 4.984 32.755 1202 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.83 % Allowed : 14.13 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1102 helix: 0.77 (0.46), residues: 142 sheet: -0.30 (0.27), residues: 352 loop : -1.50 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 298 TYR 0.019 0.001 TYR O 308 PHE 0.014 0.001 PHE N 328 TRP 0.008 0.001 TRP O 170 HIS 0.004 0.001 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 8811) covalent geometry : angle 0.59377 / 0.31 (11992) SS BOND : bond 0.00317 / 0.18 ( 16) SS BOND : angle 2.15475 / 1.98 ( 32) hydrogen bonds : bond 0.03159 / 2.06 ( 298) hydrogen bonds : angle 5.05868 / 3.48 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: K 166 LYS cc_start: 0.7585 (tttt) cc_final: 0.7260 (pttt) REVERT: K 267 TYR cc_start: 0.7704 (t80) cc_final: 0.7366 (t80) REVERT: N 9 TYR cc_start: 0.8302 (m-80) cc_final: 0.7996 (m-80) REVERT: N 42 ASP cc_start: 0.8213 (m-30) cc_final: 0.7996 (m-30) REVERT: N 66 MET cc_start: 0.9441 (ttt) cc_final: 0.9106 (ttt) REVERT: N 88 ARG cc_start: 0.8691 (mtm110) cc_final: 0.6815 (mtt180) REVERT: N 113 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8380 (mt-10) REVERT: N 173 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7227 (mm-30) REVERT: N 197 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7298 (tt) REVERT: N 365 MET cc_start: 0.8477 (ttt) cc_final: 0.7462 (pmt) REVERT: O 24 TYR cc_start: 0.8610 (m-80) cc_final: 0.8358 (m-80) REVERT: O 175 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7734 (mtp-110) REVERT: O 409 TRP cc_start: 0.8656 (m100) cc_final: 0.8233 (m100) outliers start: 36 outliers final: 19 residues processed: 134 average time/residue: 0.4596 time to fit residues: 66.1052 Evaluate side-chains 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN K 211 ASN O 386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100262 restraints weight = 11028.899| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.60 r_work: 0.2922 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8827 Z= 0.263 Angle : 0.716 9.675 12024 Z= 0.367 Chirality : 0.050 0.275 1329 Planarity : 0.006 0.072 1549 Dihedral : 5.540 37.285 1202 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.42 % Allowed : 13.07 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1102 helix: 0.88 (0.46), residues: 145 sheet: -0.07 (0.27), residues: 349 loop : -1.49 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 298 TYR 0.020 0.002 TYR O 308 PHE 0.019 0.002 PHE N 278 TRP 0.010 0.002 TRP K 202 HIS 0.008 0.002 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.26 ( 8811) covalent geometry : angle 0.70598 / 0.36 (11992) SS BOND : bond 0.00507 / 0.30 ( 16) SS BOND : angle 2.39747 / 2.04 ( 32) hydrogen bonds : bond 0.03457 / 2.19 ( 298) hydrogen bonds : angle 5.10040 / 3.53 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7668 (ptp) cc_final: 0.7014 (ptt) REVERT: K 121 LYS cc_start: 0.8305 (pptt) cc_final: 0.8092 (tmmt) REVERT: K 196 PRO cc_start: 0.8456 (Cg_endo) cc_final: 0.8174 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8333 (t80) cc_final: 0.7950 (t80) REVERT: N 66 MET cc_start: 0.9523 (ttt) cc_final: 0.9285 (ttt) REVERT: N 88 ARG cc_start: 0.8745 (mtm110) cc_final: 0.6946 (mtt180) REVERT: N 160 ASN cc_start: 0.6786 (t0) cc_final: 0.6495 (t0) REVERT: N 173 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7144 (mm-30) REVERT: N 207 ILE cc_start: 0.8167 (mt) cc_final: 0.7888 (tp) REVERT: N 239 ASN cc_start: 0.8081 (t0) cc_final: 0.7455 (t0) REVERT: N 365 MET cc_start: 0.8405 (ttt) cc_final: 0.7442 (pmt) REVERT: O 2 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8306 (mm-30) REVERT: O 18 ILE cc_start: 0.8821 (pt) cc_final: 0.8576 (pp) REVERT: O 95 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7358 (p90) REVERT: O 166 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8911 (tp) REVERT: O 175 ARG cc_start: 0.8256 (ttp80) cc_final: 0.8023 (ttp-110) REVERT: O 409 TRP cc_start: 0.8687 (m100) cc_final: 0.8387 (m100) REVERT: O 434 TYR cc_start: 0.7446 (t80) cc_final: 0.7236 (t80) outliers start: 51 outliers final: 26 residues processed: 156 average time/residue: 0.4518 time to fit residues: 75.9760 Evaluate side-chains 141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102168 restraints weight = 11155.121| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.63 r_work: 0.2947 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8827 Z= 0.146 Angle : 0.615 9.324 12024 Z= 0.316 Chirality : 0.046 0.257 1329 Planarity : 0.005 0.068 1549 Dihedral : 5.152 34.485 1202 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.14 % Allowed : 14.77 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1102 helix: 1.24 (0.48), residues: 142 sheet: 0.10 (0.28), residues: 344 loop : -1.26 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 407 TYR 0.022 0.001 TYR O 308 PHE 0.016 0.001 PHE K 128 TRP 0.007 0.001 TRP O 89 HIS 0.004 0.001 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8811) covalent geometry : angle 0.60742 / 0.31 (11992) SS BOND : bond 0.00482 / 0.31 ( 16) SS BOND : angle 1.97321 / 1.54 ( 32) hydrogen bonds : bond 0.02915 / 1.87 ( 298) hydrogen bonds : angle 4.94911 / 3.41 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7639 (ptp) cc_final: 0.7107 (ptt) REVERT: K 196 PRO cc_start: 0.8469 (Cg_endo) cc_final: 0.8221 (Cg_exo) REVERT: K 242 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (mt) REVERT: K 261 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7530 (mttt) REVERT: K 267 TYR cc_start: 0.8278 (t80) cc_final: 0.7960 (t80) REVERT: K 270 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7269 (pm20) REVERT: M 36 MET cc_start: 0.8943 (ttt) cc_final: 0.8587 (ttt) REVERT: N 66 MET cc_start: 0.9477 (ttt) cc_final: 0.9194 (ttt) REVERT: N 76 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: N 88 ARG cc_start: 0.8782 (mtm110) cc_final: 0.6965 (mtt180) REVERT: N 160 ASN cc_start: 0.6855 (t0) cc_final: 0.6572 (t0) REVERT: N 173 GLU cc_start: 0.7823 (mt-10) cc_final: 0.6982 (mm-30) REVERT: N 207 ILE cc_start: 0.8234 (mt) cc_final: 0.7899 (tp) REVERT: N 365 MET cc_start: 0.8415 (ttt) cc_final: 0.7433 (pmt) REVERT: N 407 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7375 (ttp-110) REVERT: O 2 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: O 18 ILE cc_start: 0.8737 (pt) cc_final: 0.8501 (pp) REVERT: O 24 TYR cc_start: 0.8890 (m-80) cc_final: 0.8636 (m-80) REVERT: O 88 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8838 (mmm) REVERT: O 95 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7258 (p90) REVERT: O 175 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8064 (ttp-110) REVERT: O 409 TRP cc_start: 0.8708 (m100) cc_final: 0.8481 (m100) outliers start: 39 outliers final: 23 residues processed: 143 average time/residue: 0.4678 time to fit residues: 71.7808 Evaluate side-chains 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.0050 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN O 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101801 restraints weight = 10993.403| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.56 r_work: 0.2942 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8827 Z= 0.162 Angle : 0.626 9.489 12024 Z= 0.320 Chirality : 0.046 0.195 1329 Planarity : 0.005 0.065 1549 Dihedral : 5.102 33.833 1202 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.68 % Allowed : 15.30 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1102 helix: 1.38 (0.48), residues: 142 sheet: 0.20 (0.29), residues: 324 loop : -1.24 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 298 TYR 0.021 0.002 TYR O 308 PHE 0.022 0.001 PHE K 128 TRP 0.007 0.001 TRP O 89 HIS 0.005 0.001 HIS N 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 ( 8811) covalent geometry : angle 0.61891 / 0.32 (11992) SS BOND : bond 0.00417 / 0.26 ( 16) SS BOND : angle 1.88640 / 1.45 ( 32) hydrogen bonds : bond 0.02920 / 1.85 ( 298) hydrogen bonds : angle 4.85032 / 3.34 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7622 (ptp) cc_final: 0.7282 (ptt) REVERT: K 196 PRO cc_start: 0.8126 (Cg_endo) cc_final: 0.7871 (Cg_exo) REVERT: K 242 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8369 (mt) REVERT: K 261 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7538 (mttt) REVERT: K 267 TYR cc_start: 0.8325 (t80) cc_final: 0.8023 (t80) REVERT: K 270 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7378 (pm20) REVERT: M 36 MET cc_start: 0.8968 (ttt) cc_final: 0.8603 (ttt) REVERT: N 66 MET cc_start: 0.9517 (ttp) cc_final: 0.9293 (ttt) REVERT: N 76 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: N 88 ARG cc_start: 0.8790 (mtm110) cc_final: 0.6982 (mtt180) REVERT: N 160 ASN cc_start: 0.6774 (t0) cc_final: 0.6513 (t0) REVERT: N 207 ILE cc_start: 0.8198 (mt) cc_final: 0.7838 (tp) REVERT: N 215 LYS cc_start: 0.7348 (tppp) cc_final: 0.7104 (tptm) REVERT: N 365 MET cc_start: 0.8353 (ttt) cc_final: 0.7413 (pmt) REVERT: O 2 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8325 (mm-30) REVERT: O 18 ILE cc_start: 0.8753 (pt) cc_final: 0.8533 (pp) REVERT: O 24 TYR cc_start: 0.8886 (m-80) cc_final: 0.8639 (m-80) REVERT: O 95 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7239 (p90) REVERT: O 175 ARG cc_start: 0.8214 (ttp80) cc_final: 0.8011 (ttp-110) REVERT: O 434 TYR cc_start: 0.7448 (t80) cc_final: 0.7224 (t80) outliers start: 44 outliers final: 28 residues processed: 135 average time/residue: 0.4474 time to fit residues: 64.7985 Evaluate side-chains 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.101539 restraints weight = 11161.569| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.59 r_work: 0.2950 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8827 Z= 0.154 Angle : 0.612 9.279 12024 Z= 0.313 Chirality : 0.046 0.202 1329 Planarity : 0.005 0.066 1549 Dihedral : 5.069 34.169 1202 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.14 % Allowed : 15.94 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1102 helix: 1.37 (0.47), residues: 143 sheet: 0.21 (0.29), residues: 324 loop : -1.18 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 298 TYR 0.020 0.001 TYR O 308 PHE 0.023 0.001 PHE K 128 TRP 0.008 0.001 TRP O 89 HIS 0.005 0.001 HIS N 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 ( 8811) covalent geometry : angle 0.60795 / 0.31 (11992) SS BOND : bond 0.00446 / 0.30 ( 16) SS BOND : angle 1.44091 / 1.17 ( 32) hydrogen bonds : bond 0.02885 / 1.84 ( 298) hydrogen bonds : angle 4.80468 / 3.31 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7684 (ptp) cc_final: 0.7263 (ptt) REVERT: K 196 PRO cc_start: 0.8114 (Cg_endo) cc_final: 0.7831 (Cg_exo) REVERT: K 242 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8443 (mt) REVERT: K 261 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7542 (mttt) REVERT: K 267 TYR cc_start: 0.8386 (t80) cc_final: 0.8115 (t80) REVERT: N 66 MET cc_start: 0.9509 (ttp) cc_final: 0.9295 (ttt) REVERT: N 88 ARG cc_start: 0.8752 (mtm110) cc_final: 0.6946 (mtt180) REVERT: N 160 ASN cc_start: 0.6635 (t0) cc_final: 0.6360 (t0) REVERT: N 365 MET cc_start: 0.8507 (ttt) cc_final: 0.7501 (pmt) REVERT: O 2 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8383 (mm-30) REVERT: O 18 ILE cc_start: 0.8747 (pt) cc_final: 0.8521 (pp) REVERT: O 24 TYR cc_start: 0.8884 (m-80) cc_final: 0.8643 (m-80) REVERT: O 95 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7203 (p90) REVERT: O 175 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7901 (ttp-110) REVERT: O 434 TYR cc_start: 0.7382 (t80) cc_final: 0.7173 (t80) outliers start: 39 outliers final: 31 residues processed: 133 average time/residue: 0.4558 time to fit residues: 65.5237 Evaluate side-chains 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 425 LEU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.0370 chunk 11 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106311 restraints weight = 10987.749| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.62 r_work: 0.3015 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8827 Z= 0.092 Angle : 0.549 8.631 12024 Z= 0.282 Chirality : 0.044 0.169 1329 Planarity : 0.005 0.070 1549 Dihedral : 4.649 34.814 1202 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.55 % Allowed : 17.43 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1102 helix: 1.51 (0.47), residues: 144 sheet: 0.33 (0.30), residues: 316 loop : -1.09 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 175 TYR 0.016 0.001 TYR O 308 PHE 0.019 0.001 PHE K 128 TRP 0.009 0.001 TRP O 89 HIS 0.004 0.001 HIS N 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 8811) covalent geometry : angle 0.54619 / 0.28 (11992) SS BOND : bond 0.00359 / 0.26 ( 16) SS BOND : angle 1.23775 / 0.97 ( 32) hydrogen bonds : bond 0.02474 / 1.59 ( 298) hydrogen bonds : angle 4.56560 / 3.12 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7677 (ptp) cc_final: 0.7265 (ptt) REVERT: K 196 PRO cc_start: 0.8044 (Cg_endo) cc_final: 0.7826 (Cg_exo) REVERT: K 257 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8346 (ptp) REVERT: K 261 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7687 (mttt) REVERT: K 267 TYR cc_start: 0.8312 (t80) cc_final: 0.8058 (t80) REVERT: K 270 GLU cc_start: 0.7412 (pt0) cc_final: 0.7014 (pm20) REVERT: N 66 MET cc_start: 0.9396 (ttp) cc_final: 0.9098 (ttt) REVERT: N 88 ARG cc_start: 0.8703 (mtm110) cc_final: 0.6926 (mtt180) REVERT: N 113 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8474 (mt-10) REVERT: N 365 MET cc_start: 0.8261 (ttt) cc_final: 0.7386 (pmt) REVERT: O 2 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: O 18 ILE cc_start: 0.8651 (pt) cc_final: 0.8435 (pp) REVERT: O 24 TYR cc_start: 0.8761 (m-80) cc_final: 0.8484 (m-80) REVERT: O 175 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7904 (ttp-110) outliers start: 24 outliers final: 14 residues processed: 133 average time/residue: 0.5467 time to fit residues: 77.7268 Evaluate side-chains 120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 40 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101892 restraints weight = 11100.697| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.58 r_work: 0.2950 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8827 Z= 0.154 Angle : 0.615 11.508 12024 Z= 0.312 Chirality : 0.046 0.174 1329 Planarity : 0.005 0.068 1549 Dihedral : 4.916 35.575 1202 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.44 % Allowed : 18.38 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1102 helix: 1.64 (0.48), residues: 138 sheet: 0.30 (0.29), residues: 323 loop : -1.08 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 21 TYR 0.019 0.002 TYR O 308 PHE 0.023 0.001 PHE K 128 TRP 0.007 0.001 TRP K 202 HIS 0.004 0.001 HIS N 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 ( 8811) covalent geometry : angle 0.60949 / 0.31 (11992) SS BOND : bond 0.00302 / 0.19 ( 16) SS BOND : angle 1.65605 / 1.25 ( 32) hydrogen bonds : bond 0.02843 / 1.79 ( 298) hydrogen bonds : angle 4.65509 / 3.18 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7707 (ptp) cc_final: 0.7279 (ptt) REVERT: K 257 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8319 (ptp) REVERT: K 261 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7703 (mttt) REVERT: K 267 TYR cc_start: 0.8363 (t80) cc_final: 0.8089 (t80) REVERT: N 21 ARG cc_start: 0.7908 (mmt90) cc_final: 0.5798 (mmm160) REVERT: N 42 ASP cc_start: 0.8085 (m-30) cc_final: 0.7765 (m-30) REVERT: N 88 ARG cc_start: 0.8764 (mtm110) cc_final: 0.6956 (mtt180) REVERT: N 365 MET cc_start: 0.8244 (ttt) cc_final: 0.7379 (pmt) REVERT: O 2 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: O 18 ILE cc_start: 0.8726 (pt) cc_final: 0.8496 (pp) REVERT: O 24 TYR cc_start: 0.8831 (m-80) cc_final: 0.8571 (m-80) REVERT: O 175 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7868 (ttp-110) REVERT: O 434 TYR cc_start: 0.7347 (t80) cc_final: 0.7114 (t80) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.4895 time to fit residues: 66.4311 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN N 60 ASN O 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100339 restraints weight = 11008.152| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.60 r_work: 0.2918 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8827 Z= 0.196 Angle : 0.651 11.557 12024 Z= 0.332 Chirality : 0.047 0.183 1329 Planarity : 0.005 0.067 1549 Dihedral : 5.188 35.994 1202 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.44 % Allowed : 18.38 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1102 helix: 1.55 (0.48), residues: 138 sheet: 0.20 (0.29), residues: 329 loop : -1.13 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 298 TYR 0.019 0.002 TYR O 308 PHE 0.026 0.002 PHE K 128 TRP 0.010 0.001 TRP O 409 HIS 0.006 0.001 HIS N 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 ( 8811) covalent geometry : angle 0.64479 / 0.33 (11992) SS BOND : bond 0.00308 / 0.18 ( 16) SS BOND : angle 1.81642 / 1.39 ( 32) hydrogen bonds : bond 0.03034 / 1.92 ( 298) hydrogen bonds : angle 4.82249 / 3.30 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7904 (ptp) cc_final: 0.7418 (ptt) REVERT: K 261 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7549 (mttt) REVERT: K 267 TYR cc_start: 0.8444 (t80) cc_final: 0.8236 (t80) REVERT: N 42 ASP cc_start: 0.8156 (m-30) cc_final: 0.7808 (m-30) REVERT: N 66 MET cc_start: 0.9452 (ttt) cc_final: 0.9156 (ttt) REVERT: N 88 ARG cc_start: 0.8749 (mtm110) cc_final: 0.6923 (mtt180) REVERT: N 256 HIS cc_start: 0.7795 (p90) cc_final: 0.7461 (p90) REVERT: N 365 MET cc_start: 0.8356 (ttt) cc_final: 0.7316 (pmt) REVERT: O 2 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8382 (mm-30) REVERT: O 18 ILE cc_start: 0.8788 (pt) cc_final: 0.8571 (pp) REVERT: O 24 TYR cc_start: 0.8892 (m-80) cc_final: 0.8653 (m-80) REVERT: O 175 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7899 (ttp-110) REVERT: O 434 TYR cc_start: 0.7418 (t80) cc_final: 0.7138 (t80) outliers start: 23 outliers final: 20 residues processed: 123 average time/residue: 0.4915 time to fit residues: 65.0083 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 197 GLN N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099788 restraints weight = 11081.236| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.60 r_work: 0.2917 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8827 Z= 0.210 Angle : 0.664 12.086 12024 Z= 0.339 Chirality : 0.047 0.183 1329 Planarity : 0.005 0.068 1549 Dihedral : 5.311 36.299 1202 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.55 % Allowed : 18.70 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.25), residues: 1102 helix: 1.50 (0.48), residues: 138 sheet: 0.20 (0.29), residues: 329 loop : -1.15 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 298 TYR 0.018 0.002 TYR O 308 PHE 0.028 0.002 PHE K 128 TRP 0.009 0.001 TRP O 409 HIS 0.006 0.001 HIS N 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.21 ( 8811) covalent geometry : angle 0.65826 / 0.34 (11992) SS BOND : bond 0.00318 / 0.19 ( 16) SS BOND : angle 1.83232 / 1.41 ( 32) hydrogen bonds : bond 0.03129 / 1.98 ( 298) hydrogen bonds : angle 4.86815 / 3.34 ( 807) =============================================================================== Job complete usr+sys time: 3434.26 seconds wall clock time: 59 minutes 2.17 seconds (3542.17 seconds total)