Starting phenix.real_space_refine on Tue Mar 3 19:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffn_31569/03_2026/7ffn_31569_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffn_31569/03_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_31569/03_2026/7ffn_31569_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_2026/7ffn_31569_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_2026/7ffn_31569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.25 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: 0.70 Conformation dependent library (CDL) restraints added in 321.3 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: 0.35 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: 1.28 Time building geometry restraints manager: 0.97 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: 0.010 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 covalent geometry : bond 0.00745 ( 8811) covalent geometry : angle 0.94538 (11992) SS BOND : bond 0.23452 ( 16) SS BOND : angle 6.85804 ( 32) hydrogen bonds : bond 0.21044 ( 298) hydrogen bonds : angle 8.76345 ( 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 : 0.332 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: 0.5531 time to fit residues: 122.5141 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 : 0.318 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110962 restraints weight = 11128.344| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.67 r_work: 0.3079 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8827 Z= 0.123 Angle : 0.593 8.475 12024 Z= 0.310 Chirality : 0.044 0.161 1329 Planarity : 0.006 0.082 1549 Dihedral : 5.566 48.878 1207 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.19 % Allowed : 10.41 % Favored : 86.40 % 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: -1.67 (0.24), residues: 1102 helix: 0.69 (0.46), residues: 126 sheet: -0.65 (0.27), residues: 356 loop : -1.83 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 267 TYR 0.019 0.001 TYR O 308 PHE 0.014 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 covalent geometry : bond 0.00283 ( 8811) covalent geometry : angle 0.58977 (11992) SS BOND : bond 0.00646 ( 16) SS BOND : angle 1.29954 ( 32) hydrogen bonds : bond 0.03225 ( 298) hydrogen bonds : angle 5.60413 ( 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 171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.364 Fit side-chains REVERT: K 166 LYS cc_start: 0.7464 (tttt) cc_final: 0.7231 (pttt) REVERT: K 209 TYR cc_start: 0.8466 (t80) cc_final: 0.7815 (t80) REVERT: N 9 TYR cc_start: 0.8426 (m-80) cc_final: 0.8076 (m-80) REVERT: N 21 ARG cc_start: 0.7959 (mmt90) cc_final: 0.5641 (mmm-85) REVERT: N 66 MET cc_start: 0.9430 (ttt) cc_final: 0.9096 (ttt) REVERT: N 76 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: N 88 ARG cc_start: 0.8450 (mtm110) cc_final: 0.6547 (mtt180) REVERT: N 113 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: N 173 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7289 (mm-30) REVERT: N 290 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8053 (tttm) REVERT: N 365 MET cc_start: 0.8456 (ttt) cc_final: 0.7475 (pmt) REVERT: N 398 THR cc_start: 0.8580 (m) cc_final: 0.8196 (p) REVERT: O 13 ILE cc_start: 0.9268 (mt) cc_final: 0.9047 (mm) REVERT: O 24 TYR cc_start: 0.8480 (m-80) cc_final: 0.8206 (m-80) REVERT: O 115 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8486 (tp) REVERT: O 144 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8778 (p) REVERT: O 175 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7609 (ttp-110) REVERT: O 281 ASP cc_start: 0.8362 (t0) cc_final: 0.8123 (t70) REVERT: O 345 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: O 409 TRP cc_start: 0.8520 (m100) cc_final: 0.8181 (m100) outliers start: 30 outliers final: 11 residues processed: 156 average time/residue: 0.5825 time to fit residues: 96.6159 Evaluate side-chains 127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU 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 144 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 345 GLU 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: 0.7980 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 0.0470 overall best weight: 3.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN N 152 GLN N 159 GLN N 358 HIS O 130 GLN O 155 ASN O 386 HIS O 439 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102865 restraints weight = 10899.480| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.60 r_work: 0.2967 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 8827 Z= 0.202 Angle : 0.668 13.347 12024 Z= 0.344 Chirality : 0.047 0.252 1329 Planarity : 0.006 0.075 1549 Dihedral : 5.280 32.356 1202 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.46 % Allowed : 13.39 % Favored : 82.15 % 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: -1.20 (0.24), residues: 1102 helix: 0.80 (0.46), residues: 142 sheet: -0.35 (0.27), residues: 362 loop : -1.51 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 298 TYR 0.022 0.002 TYR O 308 PHE 0.017 0.002 PHE N 278 TRP 0.010 0.002 TRP K 202 HIS 0.007 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 8811) covalent geometry : angle 0.66150 (11992) SS BOND : bond 0.00553 ( 16) SS BOND : angle 1.88285 ( 32) hydrogen bonds : bond 0.03512 ( 298) hydrogen bonds : angle 5.11423 ( 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 164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7806 (ptp) cc_final: 0.7429 (ptt) REVERT: K 121 LYS cc_start: 0.8231 (pptt) cc_final: 0.7992 (tmmt) REVERT: K 267 TYR cc_start: 0.7957 (t80) cc_final: 0.7502 (t80) REVERT: N 9 TYR cc_start: 0.8412 (m-80) cc_final: 0.8191 (m-80) REVERT: N 66 MET cc_start: 0.9460 (ttt) cc_final: 0.9177 (ttt) REVERT: N 88 ARG cc_start: 0.8798 (mtm110) cc_final: 0.6843 (mtt180) REVERT: N 173 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7197 (mm-30) REVERT: N 197 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7336 (tt) REVERT: N 365 MET cc_start: 0.8521 (ttt) cc_final: 0.7490 (pmt) REVERT: O 24 TYR cc_start: 0.8801 (m-80) cc_final: 0.8565 (m-80) REVERT: O 95 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7430 (p90) REVERT: O 175 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7658 (ttp-110) REVERT: O 409 TRP cc_start: 0.8599 (m100) cc_final: 0.8172 (m100) outliers start: 42 outliers final: 17 residues processed: 148 average time/residue: 0.5100 time to fit residues: 80.9394 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain N residue 20 ILE 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 95 PHE 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 208 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103131 restraints weight = 11109.555| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.62 r_work: 0.2971 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8827 Z= 0.172 Angle : 0.628 9.061 12024 Z= 0.322 Chirality : 0.047 0.257 1329 Planarity : 0.005 0.071 1549 Dihedral : 5.189 34.102 1202 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.57 % Allowed : 14.13 % Favored : 81.30 % 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: -0.88 (0.25), residues: 1102 helix: 1.16 (0.47), residues: 141 sheet: -0.02 (0.28), residues: 347 loop : -1.38 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 298 TYR 0.021 0.002 TYR O 308 PHE 0.015 0.001 PHE N 328 TRP 0.007 0.001 TRP N 330 HIS 0.005 0.001 HIS O 386 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8811) covalent geometry : angle 0.62026 (11992) SS BOND : bond 0.00492 ( 16) SS BOND : angle 2.04983 ( 32) hydrogen bonds : bond 0.03044 ( 298) hydrogen bonds : angle 4.94050 ( 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 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7704 (ptp) cc_final: 0.7110 (ptt) REVERT: K 121 LYS cc_start: 0.8249 (pptt) cc_final: 0.7994 (tmmt) REVERT: K 151 MET cc_start: 0.8676 (mmm) cc_final: 0.8457 (mtp) REVERT: K 166 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7644 (ttmt) REVERT: K 176 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: K 223 LYS cc_start: 0.8689 (tptp) cc_final: 0.8441 (tppt) REVERT: K 267 TYR cc_start: 0.8186 (t80) cc_final: 0.7753 (t80) REVERT: K 270 GLU cc_start: 0.6591 (pm20) cc_final: 0.6363 (pm20) REVERT: N 9 TYR cc_start: 0.8385 (m-80) cc_final: 0.8167 (m-80) REVERT: N 66 MET cc_start: 0.9476 (ttt) cc_final: 0.9230 (ttt) REVERT: N 88 ARG cc_start: 0.8801 (mtm110) cc_final: 0.7006 (mtt180) REVERT: N 173 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7175 (mm-30) REVERT: N 197 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7110 (tt) REVERT: N 365 MET cc_start: 0.8362 (ttt) cc_final: 0.7446 (pmt) REVERT: O 18 ILE cc_start: 0.8791 (pt) cc_final: 0.8544 (pp) REVERT: O 24 TYR cc_start: 0.8847 (m-80) cc_final: 0.8581 (m-80) REVERT: O 95 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7428 (p90) REVERT: O 175 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7740 (ttp-110) REVERT: O 409 TRP cc_start: 0.8664 (m100) cc_final: 0.8363 (m100) outliers start: 43 outliers final: 23 residues processed: 142 average time/residue: 0.5264 time to fit residues: 79.9633 Evaluate side-chains 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 176 GLU Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 20 ILE 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 63 CYS Chi-restraints excluded: chain O residue 80 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 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 72 optimal weight: 0.0040 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107289 restraints weight = 11198.271| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.61 r_work: 0.3037 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3691 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= 0.097 Angle : 0.563 10.397 12024 Z= 0.289 Chirality : 0.044 0.234 1329 Planarity : 0.005 0.068 1549 Dihedral : 4.829 33.025 1202 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.51 % Allowed : 15.20 % Favored : 81.30 % 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: 1.33 (0.47), residues: 142 sheet: 0.25 (0.29), residues: 335 loop : -1.21 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 267 TYR 0.020 0.001 TYR O 308 PHE 0.011 0.001 PHE K 128 TRP 0.007 0.001 TRP N 326 HIS 0.002 0.000 HIS N 256 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8811) covalent geometry : angle 0.55767 (11992) SS BOND : bond 0.00557 ( 16) SS BOND : angle 1.63755 ( 32) hydrogen bonds : bond 0.02597 ( 298) hydrogen bonds : angle 4.76706 ( 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 152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7567 (ptp) cc_final: 0.7000 (ptt) REVERT: K 121 LYS cc_start: 0.8274 (pptt) cc_final: 0.8043 (tmmt) REVERT: K 166 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7902 (ttmt) REVERT: K 267 TYR cc_start: 0.8103 (t80) cc_final: 0.7657 (t80) REVERT: K 270 GLU cc_start: 0.6613 (pm20) cc_final: 0.6291 (pm20) REVERT: N 9 TYR cc_start: 0.8288 (m-80) cc_final: 0.8081 (m-80) REVERT: N 66 MET cc_start: 0.9366 (ttt) cc_final: 0.9077 (ttt) REVERT: N 88 ARG cc_start: 0.8687 (mtm110) cc_final: 0.6955 (mtt180) REVERT: N 113 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8525 (mt-10) REVERT: N 365 MET cc_start: 0.8303 (ttt) cc_final: 0.7430 (pmt) REVERT: O 18 ILE cc_start: 0.8737 (pt) cc_final: 0.8523 (pp) REVERT: O 24 TYR cc_start: 0.8746 (m-80) cc_final: 0.8441 (m-80) REVERT: O 175 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7703 (ttp-110) REVERT: O 281 ASP cc_start: 0.8567 (t70) cc_final: 0.8354 (t0) REVERT: O 409 TRP cc_start: 0.8678 (m100) cc_final: 0.8413 (m100) outliers start: 33 outliers final: 17 residues processed: 141 average time/residue: 0.4685 time to fit residues: 70.7895 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 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 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 133 LEU Chi-restraints excluded: chain O residue 213 LEU 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: 0.0970 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103680 restraints weight = 11066.327| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.74 r_work: 0.2971 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8827 Z= 0.149 Angle : 0.599 8.096 12024 Z= 0.307 Chirality : 0.046 0.191 1329 Planarity : 0.005 0.064 1549 Dihedral : 4.897 33.415 1202 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.40 % Allowed : 15.41 % Favored : 81.19 % 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: -0.54 (0.25), residues: 1102 helix: 1.44 (0.48), residues: 143 sheet: 0.24 (0.29), residues: 327 loop : -1.14 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 298 TYR 0.020 0.001 TYR O 308 PHE 0.014 0.001 PHE K 128 TRP 0.008 0.001 TRP K 202 HIS 0.004 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8811) covalent geometry : angle 0.59312 (11992) SS BOND : bond 0.00399 ( 16) SS BOND : angle 1.72827 ( 32) hydrogen bonds : bond 0.02826 ( 298) hydrogen bonds : angle 4.68715 ( 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 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7619 (ptp) cc_final: 0.7117 (ptt) REVERT: K 121 LYS cc_start: 0.8434 (pptt) cc_final: 0.8205 (tmmt) REVERT: K 166 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7941 (ttmt) REVERT: K 267 TYR cc_start: 0.8256 (t80) cc_final: 0.7909 (t80) REVERT: K 270 GLU cc_start: 0.6562 (pm20) cc_final: 0.6254 (pm20) REVERT: N 9 TYR cc_start: 0.8355 (m-80) cc_final: 0.8130 (m-80) REVERT: N 21 ARG cc_start: 0.7949 (mmt90) cc_final: 0.5893 (mmm160) REVERT: N 42 ASP cc_start: 0.8090 (m-30) cc_final: 0.7759 (m-30) REVERT: N 66 MET cc_start: 0.9500 (ttp) cc_final: 0.9280 (ttt) REVERT: N 88 ARG cc_start: 0.8800 (mtm110) cc_final: 0.6987 (mtt180) REVERT: N 215 LYS cc_start: 0.7278 (tppp) cc_final: 0.7041 (tptm) REVERT: N 365 MET cc_start: 0.8408 (ttt) cc_final: 0.7464 (pmt) REVERT: O 18 ILE cc_start: 0.8749 (pt) cc_final: 0.8529 (pp) REVERT: O 24 TYR cc_start: 0.8822 (m-80) cc_final: 0.8558 (m-80) REVERT: O 175 ARG cc_start: 0.8214 (ttp80) cc_final: 0.8006 (ttp-110) REVERT: O 177 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8544 (mm) REVERT: O 209 SER cc_start: 0.9002 (m) cc_final: 0.8559 (p) REVERT: O 409 TRP cc_start: 0.8792 (m100) cc_final: 0.8584 (m100) outliers start: 32 outliers final: 23 residues processed: 135 average time/residue: 0.5362 time to fit residues: 77.3888 Evaluate side-chains 135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 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 394 VAL 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 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 177 ILE Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 348 GLU 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: 0.0070 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3682 r_free = 0.3682 target = 0.146713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104322 restraints weight = 11239.527| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.75 r_work: 0.2956 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8827 Z= 0.124 Angle : 0.582 9.389 12024 Z= 0.297 Chirality : 0.045 0.177 1329 Planarity : 0.005 0.065 1549 Dihedral : 4.878 33.447 1202 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.87 % Allowed : 16.68 % Favored : 80.45 % 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: -0.48 (0.25), residues: 1102 helix: 1.44 (0.47), residues: 144 sheet: 0.33 (0.29), residues: 317 loop : -1.10 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 149 TYR 0.024 0.001 TYR O 434 PHE 0.013 0.001 PHE K 128 TRP 0.006 0.001 TRP N 330 HIS 0.003 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8811) covalent geometry : angle 0.57828 (11992) SS BOND : bond 0.00384 ( 16) SS BOND : angle 1.34235 ( 32) hydrogen bonds : bond 0.02723 ( 298) hydrogen bonds : angle 4.63209 ( 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 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7792 (ptp) cc_final: 0.7277 (ptt) REVERT: K 121 LYS cc_start: 0.8339 (pptt) cc_final: 0.8131 (tmmt) REVERT: K 166 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7789 (ttmt) REVERT: K 267 TYR cc_start: 0.8284 (t80) cc_final: 0.7963 (t80) REVERT: K 270 GLU cc_start: 0.6561 (pm20) cc_final: 0.6270 (pm20) REVERT: N 21 ARG cc_start: 0.7820 (mmt90) cc_final: 0.5554 (mmm-85) REVERT: N 88 ARG cc_start: 0.8793 (mtm110) cc_final: 0.6999 (mtt180) REVERT: N 215 LYS cc_start: 0.7156 (tppp) cc_final: 0.6934 (tptm) REVERT: N 365 MET cc_start: 0.8427 (ttt) cc_final: 0.7448 (pmt) REVERT: O 18 ILE cc_start: 0.8727 (pt) cc_final: 0.8505 (pp) REVERT: O 24 TYR cc_start: 0.8816 (m-80) cc_final: 0.8499 (m-80) REVERT: O 175 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7957 (ttp-110) REVERT: O 209 SER cc_start: 0.9018 (m) cc_final: 0.8591 (p) outliers start: 27 outliers final: 23 residues processed: 131 average time/residue: 0.5612 time to fit residues: 78.6241 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR 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 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 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 213 LEU 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: 7.9990 chunk 11 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101857 restraints weight = 11016.584| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.61 r_work: 0.2931 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8827 Z= 0.187 Angle : 0.642 9.157 12024 Z= 0.328 Chirality : 0.047 0.180 1329 Planarity : 0.005 0.064 1549 Dihedral : 5.097 34.353 1202 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.29 % Allowed : 17.00 % Favored : 79.70 % 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: -0.49 (0.25), residues: 1102 helix: 1.43 (0.47), residues: 144 sheet: 0.28 (0.29), residues: 327 loop : -1.11 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 46 TYR 0.020 0.002 TYR O 308 PHE 0.024 0.002 PHE K 128 TRP 0.007 0.001 TRP K 202 HIS 0.006 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8811) covalent geometry : angle 0.63716 (11992) SS BOND : bond 0.00420 ( 16) SS BOND : angle 1.65763 ( 32) hydrogen bonds : bond 0.03019 ( 298) hydrogen bonds : angle 4.75632 ( 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 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7748 (ptp) cc_final: 0.7173 (ptt) REVERT: K 121 LYS cc_start: 0.8338 (pptt) cc_final: 0.8117 (tmmt) REVERT: K 166 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7819 (ttmt) REVERT: K 267 TYR cc_start: 0.8403 (t80) cc_final: 0.8116 (t80) REVERT: K 270 GLU cc_start: 0.6644 (pm20) cc_final: 0.6371 (pm20) REVERT: N 42 ASP cc_start: 0.8104 (m-30) cc_final: 0.7799 (m-30) REVERT: N 66 MET cc_start: 0.9428 (ttt) cc_final: 0.9162 (ttt) REVERT: N 88 ARG cc_start: 0.8783 (mtm110) cc_final: 0.6967 (mtt180) REVERT: N 120 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: N 365 MET cc_start: 0.8360 (ttt) cc_final: 0.7412 (pmt) REVERT: O 18 ILE cc_start: 0.8788 (pt) cc_final: 0.8575 (pp) REVERT: O 24 TYR cc_start: 0.8873 (m-80) cc_final: 0.8594 (m-80) REVERT: O 95 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7216 (p90) REVERT: O 175 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7844 (ttp-110) REVERT: O 209 SER cc_start: 0.9003 (m) cc_final: 0.8583 (p) outliers start: 31 outliers final: 24 residues processed: 131 average time/residue: 0.4773 time to fit residues: 67.3746 Evaluate side-chains 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 247 GLU Chi-restraints excluded: chain K residue 251 THR 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 189 THR 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 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 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 348 GLU Chi-restraints excluded: chain O residue 377 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: 9.9990 chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN O 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101138 restraints weight = 11103.022| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.55 r_work: 0.2937 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8827 Z= 0.187 Angle : 0.640 9.053 12024 Z= 0.328 Chirality : 0.047 0.180 1329 Planarity : 0.005 0.067 1549 Dihedral : 5.189 35.328 1202 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.87 % Allowed : 17.64 % Favored : 79.49 % 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: -0.53 (0.25), residues: 1102 helix: 1.48 (0.48), residues: 138 sheet: 0.26 (0.29), residues: 331 loop : -1.14 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 298 TYR 0.024 0.002 TYR O 434 PHE 0.025 0.002 PHE K 128 TRP 0.008 0.001 TRP O 409 HIS 0.006 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8811) covalent geometry : angle 0.63472 (11992) SS BOND : bond 0.00382 ( 16) SS BOND : angle 1.64706 ( 32) hydrogen bonds : bond 0.03028 ( 298) hydrogen bonds : angle 4.80576 ( 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 138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7819 (ptp) cc_final: 0.7424 (ptt) REVERT: K 121 LYS cc_start: 0.8354 (pptt) cc_final: 0.8127 (tmmt) REVERT: K 166 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7829 (ttmt) REVERT: K 267 TYR cc_start: 0.8447 (t80) cc_final: 0.8180 (t80) REVERT: K 270 GLU cc_start: 0.6607 (pm20) cc_final: 0.6361 (pm20) REVERT: N 42 ASP cc_start: 0.7979 (m-30) cc_final: 0.7684 (m-30) REVERT: N 88 ARG cc_start: 0.8781 (mtm110) cc_final: 0.6959 (mtt180) REVERT: N 365 MET cc_start: 0.8503 (ttt) cc_final: 0.7498 (pmt) REVERT: O 18 ILE cc_start: 0.8786 (pt) cc_final: 0.8571 (pp) REVERT: O 24 TYR cc_start: 0.8871 (m-80) cc_final: 0.8628 (m-80) REVERT: O 95 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7209 (p90) outliers start: 27 outliers final: 23 residues processed: 129 average time/residue: 0.5059 time to fit residues: 70.3153 Evaluate side-chains 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 247 GLU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR 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 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 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 377 LYS Chi-restraints excluded: chain O residue 426 VAL 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: 0.2980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102876 restraints weight = 11089.981| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.57 r_work: 0.2953 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8827 Z= 0.131 Angle : 0.601 9.170 12024 Z= 0.308 Chirality : 0.045 0.178 1329 Planarity : 0.005 0.069 1549 Dihedral : 5.043 35.579 1202 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.76 % Allowed : 18.28 % Favored : 78.96 % 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: -0.42 (0.25), residues: 1102 helix: 1.59 (0.48), residues: 138 sheet: 0.37 (0.29), residues: 323 loop : -1.09 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 175 TYR 0.017 0.001 TYR O 308 PHE 0.024 0.001 PHE K 128 TRP 0.009 0.001 TRP O 409 HIS 0.003 0.001 HIS N 256 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8811) covalent geometry : angle 0.59753 (11992) SS BOND : bond 0.00325 ( 16) SS BOND : angle 1.39922 ( 32) hydrogen bonds : bond 0.02809 ( 298) hydrogen bonds : angle 4.70888 ( 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 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7839 (ptp) cc_final: 0.7445 (ptt) REVERT: K 121 LYS cc_start: 0.8348 (pptt) cc_final: 0.8139 (tmmt) REVERT: K 166 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7844 (ttmt) REVERT: K 261 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7691 (mttt) REVERT: K 267 TYR cc_start: 0.8408 (t80) cc_final: 0.8120 (t80) REVERT: K 270 GLU cc_start: 0.6570 (pm20) cc_final: 0.6259 (pm20) REVERT: N 88 ARG cc_start: 0.8738 (mtm110) cc_final: 0.6939 (mtt180) REVERT: N 120 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7950 (ttm-80) REVERT: N 365 MET cc_start: 0.8427 (ttt) cc_final: 0.7473 (pmt) REVERT: O 18 ILE cc_start: 0.8741 (pt) cc_final: 0.8515 (pp) REVERT: O 24 TYR cc_start: 0.8816 (m-80) cc_final: 0.8526 (m-80) REVERT: O 175 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.8012 (ttp-110) outliers start: 26 outliers final: 20 residues processed: 127 average time/residue: 0.4835 time to fit residues: 66.3022 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 251 THR 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 189 THR 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 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 104 SER Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 426 VAL 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: 4.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102765 restraints weight = 11138.312| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.61 r_work: 0.2958 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8827 Z= 0.134 Angle : 0.601 9.161 12024 Z= 0.306 Chirality : 0.045 0.175 1329 Planarity : 0.005 0.069 1549 Dihedral : 4.989 36.044 1202 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.44 % Allowed : 18.70 % Favored : 78.85 % 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: -0.39 (0.25), residues: 1102 helix: 1.55 (0.47), residues: 139 sheet: 0.39 (0.29), residues: 324 loop : -1.05 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 175 TYR 0.026 0.001 TYR O 434 PHE 0.022 0.001 PHE K 128 TRP 0.009 0.001 TRP O 409 HIS 0.004 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8811) covalent geometry : angle 0.59715 (11992) SS BOND : bond 0.00320 ( 16) SS BOND : angle 1.36509 ( 32) hydrogen bonds : bond 0.02783 ( 298) hydrogen bonds : angle 4.69533 ( 807) =============================================================================== Job complete usr+sys time: 3921.63 seconds wall clock time: 67 minutes 12.10 seconds (4032.10 seconds total)